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/7769618/working'
mkdir: created directory `/scratch/stefan/7769618/working/protonate'
Storing results in /scratch/stefan/7769618/finished
Working in /scratch/stefan/7769618/working
/scratch/stefan/7769618/working /scratch/stefan/7769618

/scratch/stefan/7769618/working/protonate /scratch/stefan/7769618/working /scratch/stefan/7769618
Precomputing protomers for all compounds (pH: 7.4)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file
mv: cannot move `/nfs/home/stefan/.install4j_new' to `/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
Nov 27, 2019 6:17:21 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:21 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:21 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:51 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:37 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:37 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:37 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:37 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 6:19:39 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:39 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:39 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:39 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:16 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:42 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:51 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:20 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:56 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:56 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:56 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:25 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:53 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 6:23:08 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 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:19 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
ph 7.4: 1241 protomers created
Coalesing and merging protomers
1223 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1223 protomers after new stereo-center expansion
/scratch/stefan/7769618/working /scratch/stefan/7769618

Bulk generating 3D conformations all protomers in /scratch/stefan/7769618/working/3D
mkdir: created directory `/scratch/stefan/7769618/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7769618/working/protonate/xaaaabl-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'
1224 3D conformations generated for 1000 compounds

Building REAL300000037001
mkdir: created directory `/scratch/stefan/7769618/working/building'
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037001'
/scratch/stefan/7769618/working/building/REAL300000037001 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037001

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037001/0 /scratch/stefan/7769618/working/building/REAL300000037001 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1
`/scratch/stefan/7769618/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037001 none CC1=CN=CC(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 51, 55, 55, 55, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 55, 55, 55, 55, 55, 55, 55, 42, 12, 1, 1, 1] 55
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037001 none CC1=CN=CC(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 55, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 2, 2, 2, 7, 35, 55, 55, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037001 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037001
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `/scratch/stefan/7769618/finished'
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037001/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037001
Building REAL300000037002
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037002'
/scratch/stefan/7769618/working/building/REAL300000037002 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037002

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037002/0 /scratch/stefan/7769618/working/building/REAL300000037002 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/2
`/scratch/stefan/7769618/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1)

`REAL300000037002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037002 none COC1=CC(C)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 92, 92, 92, 92, 92, 92, 92, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 106, 106, 106, 92, 92, 92, 92, 92, 53, 12, 1, 1, 1, 92, 92] 106
rigid atoms, others: [35, 36, 37, 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, 38, 39])
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: REAL300000037002 none COC1=CC(C)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 7, 7, 38, 92, 92, 92, 92, 92, 92, 106, 106, 92, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 1, 7, 38, 92, 92, 92, 1, 1] 106
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 22, 23, 24, 38, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 33, 34, 35, 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/7769618/working/building/REAL300000037002 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037002
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037002/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037002
Building REAL300000037003
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037003'
/scratch/stefan/7769618/working/building/REAL300000037003 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037003

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037003/0 /scratch/stefan/7769618/working/building/REAL300000037003 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/3
`/scratch/stefan/7769618/working/3D/3' -> `0.mol2'
Preparing input files

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

`REAL300000037003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037003 none CC(CC1=CN(C)N=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 5, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 8, 51, 115, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 51, 51, 51, 115, 115, 201, 201, 201, 201, 201, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 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])
total number of confs: 591
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037003 none CC(CC1=CN(C)N=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 5, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 1, 1, 24, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 24, 24, 24, 24, 9, 9, 1, 2, 2, 2, 1, 201, 201, 201] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037003 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037003
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037003/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037003
Building REAL300000037004
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037004'
/scratch/stefan/7769618/working/building/REAL300000037004 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037004

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037004/0 /scratch/stefan/7769618/working/building/REAL300000037004 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/4
`/scratch/stefan/7769618/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NC2CC3CC=CCC3C2)=CC=C1Cl)

`REAL300000037004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037004 none O=C([O-])C1=CC(N=NC2CC3CC=CCC3C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 36, 35])
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: REAL300000037004 none O=C([O-])C1=CC(N=NC2CC3CC=CCC3C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 36, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037004 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037004
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037004/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037004
Building REAL300000037005
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037005'
/scratch/stefan/7769618/working/building/REAL300000037005 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037005

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037005/0 /scratch/stefan/7769618/working/building/REAL300000037005 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/5
`/scratch/stefan/7769618/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C(F)(F)F)

`REAL300000037005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037005 none CC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [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]
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, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 46, 12, 1, 1, 1] 62
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037005 none CC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [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]
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, 9, 9, 38, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 38, 62, 62, 62] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037005 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037005
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037005/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037005
Building REAL300000037006
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037006'
/scratch/stefan/7769618/working/building/REAL300000037006 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037006

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037006/0 /scratch/stefan/7769618/working/building/REAL300000037006 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/6
`/scratch/stefan/7769618/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=N1)

`REAL300000037006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037006 none C=CCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need 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, 107, 107, 107, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 107, 107, 201, 201, 201, 197, 197, 107, 47, 11, 1, 1, 1, 107] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 629
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037006 none C=CCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 8, 1, 1, 1, 1, 1, 6, 6, 47, 107, 107, 106, 106, 107, 107, 119, 119, 107, 1, 1, 31, 31, 31, 8, 8, 1, 6, 47, 107, 107, 107, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 19, 20, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037006 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037006
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037006/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037006
Building REAL300000037007
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037007'
/scratch/stefan/7769618/working/building/REAL300000037007 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037007

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037007/0 /scratch/stefan/7769618/working/building/REAL300000037007 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/7
`/scratch/stefan/7769618/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=NNC=C3C=C2)=CC=C1Cl)

`REAL300000037007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037007 none O=C([O-])C1=CC(NN=CC2=CC3=NNC=C3C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 76, 77, 76, 76, 54, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 77, 77, 77, 76, 54, 10, 1, 1, 1, 1, 1, 76, 77] 77
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 30, 31])
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: REAL300000037007 none O=C([O-])C1=CC(NN=CC2=CC3=NNC=C3C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 10, 47, 47, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 10, 47, 76, 76, 76, 76, 76, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 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/7769618/working/building/REAL300000037007 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037007
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037007/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037007
Building REAL300000037008
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037008'
/scratch/stefan/7769618/working/building/REAL300000037008 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037008

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037008/0 /scratch/stefan/7769618/working/building/REAL300000037008 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/8
`/scratch/stefan/7769618/working/3D/8' -> `0.mol2'
Preparing input files

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

`REAL300000037008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037008 none CCC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 142, 137, 142, 102, 137, 137, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 137, 137, 157, 157, 157, 157, 157, 142, 142, 142, 142, 137, 137, 51, 11, 1, 1, 1, 137, 137] 157
rigid atoms, others: [36, 37, 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, 35, 39, 40])
total number of confs: 493
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037008 none CCC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [9, 7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 56, 137, 137, 137, 137, 137, 137, 152, 152, 137, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 1, 1, 10, 56, 137, 137, 137, 1, 1] 157
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 39, 40, 21, 22] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037008 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037008
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037008/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037008
Building REAL300000037009
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037009'
/scratch/stefan/7769618/working/building/REAL300000037009 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037009

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037009/0 /scratch/stefan/7769618/working/building/REAL300000037009 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/9
`/scratch/stefan/7769618/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=NC=C(Br)C=C3O2)=CC=C1Cl)

`REAL300000037009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037009 none O=C([O-])C1=CC(NN=CC2=CC3=NC=C(Br)C=C3O2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 59, 39, 8, 1, 1, 1, 60, 60] 60
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30])
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: REAL300000037009 none O=C([O-])C1=CC(NN=CC2=CC3=NC=C(Br)C=C3O2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 43, 43, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 10, 43, 59, 59, 59, 1, 1] 60
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])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037009 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037009
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037009/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037009
Building REAL300000037010
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037010'
/scratch/stefan/7769618/working/building/REAL300000037010 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037010

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037010/0 /scratch/stefan/7769618/working/building/REAL300000037010 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/10
`/scratch/stefan/7769618/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)=CC=C1Cl)

`REAL300000037010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037010 none O=C([O-])C1=CC(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [52, 46, 52, 46, 46, 32, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 31, 11, 12, 1, 1, 1, 46, 46] 57
rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 33, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037010 none O=C([O-])C1=CC(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 27, 27, 46, 46, 46, 46, 57, 57, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 6, 27, 57, 46, 46, 46, 1, 1] 57
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037010 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037010
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037010/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037010
Building REAL300000037011
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037011'
/scratch/stefan/7769618/working/building/REAL300000037011 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037011

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037011/0 /scratch/stefan/7769618/working/building/REAL300000037011 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/11
`/scratch/stefan/7769618/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037011 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 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, 2, 2, 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]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 41, 39, 39, 39, 19, 7, 1, 1, 1] 41
rigid atoms, others: [32, 33, 34, 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])
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: REAL300000037011 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 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, 2, 2, 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]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 24, 39, 39, 39, 39, 39, 39, 41, 41, 39, 3, 3, 3, 1, 1, 1, 10, 24, 39, 39, 39] 41
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 27, 28, 29] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037011 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037011
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037011/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037011
Building REAL300000037012
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037012'
/scratch/stefan/7769618/working/building/REAL300000037012 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037012

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037012/0 /scratch/stefan/7769618/working/building/REAL300000037012 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/12
`/scratch/stefan/7769618/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NC2CCC3(C2)CCOCC3)=CC=C1Cl)

`REAL300000037012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037012 none O=C([O-])C1=CC(N=NC2CCC3(C2)CCOCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38])
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: REAL300000037012 none O=C([O-])C1=CC(N=NC2CCC3(C2)CCOCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037012 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037012
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037012/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037012
Building REAL300000037013
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037013'
/scratch/stefan/7769618/working/building/REAL300000037013 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037013

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037013/0 /scratch/stefan/7769618/working/building/REAL300000037013 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/13
`/scratch/stefan/7769618/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=N1)

`REAL300000037013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037013 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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, 69, 140, 140, 69, 69, 69, 69, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 140, 140, 140, 69, 69, 69, 34, 9, 1, 1, 1] 140
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037013 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 7, 7, 33, 69, 69, 69, 69, 69, 69, 76, 76, 69, 1, 11, 11, 11, 1, 1, 1, 7, 33, 69, 69, 69] 140
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037013 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037013
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037013/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037013
Building REAL300000037014
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037014'
/scratch/stefan/7769618/working/building/REAL300000037014 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037014

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037014/0 /scratch/stefan/7769618/working/building/REAL300000037014 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/14
`/scratch/stefan/7769618/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(CCOC3)N=C2Cl)=CC=C1Cl)

`REAL300000037014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037014 none O=C([O-])C1=CC(NN=CC2=CC3=C(CCOC3)N=C2Cl)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 36, 9, 1, 1, 1, 1, 1, 1, 1, 52, 52] 52
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23, 24, 25, 26])
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: REAL300000037014 none O=C([O-])C1=CC(NN=CC2=CC3=C(CCOC3)N=C2Cl)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 38, 38, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 11, 38, 52, 52, 52, 52, 52, 52, 52, 1, 1] 52
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037014 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037014
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037014/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037014
Building REAL300000037015
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037015'
/scratch/stefan/7769618/working/building/REAL300000037015 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037015

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037015/0 /scratch/stefan/7769618/working/building/REAL300000037015 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/15
`/scratch/stefan/7769618/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC2=C(CCC2=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)S1)

`REAL300000037015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037015 none CC1=CC2=C(CCC2=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1] 30
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 53
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: REAL300000037015 none CC1=CC2=C(CCC2=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 30, 30, 30] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 24, 25, 26, 27, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31])
total number of confs: 51
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037015 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037015
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037015/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037015
Building REAL300000037016
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037016'
/scratch/stefan/7769618/working/building/REAL300000037016 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037016

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037016/0 /scratch/stefan/7769618/working/building/REAL300000037016 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/16
`/scratch/stefan/7769618/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1)

`REAL300000037016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037016 none COC1=CC(OC)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [94, 72, 72, 72, 72, 72, 92, 72, 72, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 72, 72, 72, 94, 94, 94, 72, 92, 92, 92, 72, 54, 12, 1, 1, 1, 72, 72] 99
rigid atoms, others: [36, 37, 38, 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, 39, 40])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037016 none COC1=CC(OC)=C2C=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 6, 6, 20, 72, 72, 72, 72, 72, 72, 78, 78, 72, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 6, 20, 72, 72, 72, 1, 1] 99
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 39, 40, 23, 24, 25, 33, 29] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037016 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037016
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037016/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037016
Building REAL300000037017
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037017'
/scratch/stefan/7769618/working/building/REAL300000037017 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037017

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037017/0 /scratch/stefan/7769618/working/building/REAL300000037017 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/17
`/scratch/stefan/7769618/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(C=CS3)N2)=CC=C1Cl)

`REAL300000037017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037017 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=CS3)N2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 47, 48, 47, 47, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 24, 5, 1, 1, 1, 1, 47, 47] 48
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 28, 29])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037017 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=CS3)N2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 35, 35, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 12, 35, 47, 47, 47, 47, 1, 1] 48
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037017 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037017
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037017/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037017
Building REAL300000037018
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037018'
/scratch/stefan/7769618/working/building/REAL300000037018 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037018

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037018/0 /scratch/stefan/7769618/working/building/REAL300000037018 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/18
`/scratch/stefan/7769618/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)=CC=C1Cl)

`REAL300000037018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037018 none O=C([O-])C1=CC(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 54, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 100, 100, 99, 99, 100, 54, 12, 1, 1, 1, 1, 1, 100, 100] 100
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 16, 17, 18, 35, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037018 none O=C([O-])C1=CC(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 54, 54, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 13, 54, 100, 100, 100, 100, 100, 1, 1] 100
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])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037018 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037018
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037018/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037018
Building REAL300000037019
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037019'
/scratch/stefan/7769618/working/building/REAL300000037019 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037019

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037019/0 /scratch/stefan/7769618/working/building/REAL300000037019 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/19
`/scratch/stefan/7769618/working/3D/19' -> `0.mol2'
Preparing input files

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

`REAL300000037019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037019 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 47, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 92, 92, 92, 1, 1, 1, 2, 2, 2] 92
rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 191
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037019 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 92, 92, 90, 92, 92, 92, 92, 47, 47, 47, 10, 1, 1, 1, 92, 92, 92, 92, 92, 92] 92
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 164
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037019 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037019
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037019/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037019
Building REAL300000037020
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037020'
/scratch/stefan/7769618/working/building/REAL300000037020 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037020

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037020/0 /scratch/stefan/7769618/working/building/REAL300000037020 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/20
`/scratch/stefan/7769618/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 47, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 47, 47, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 393
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 62, 179, 201, 201, 179, 201, 201, 62, 62, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 62, 62, 179, 179, 201, 201, 179, 201, 201, 62, 29, 29, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 729
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 14, 14, 6, 14, 14, 1, 1, 1, 1, 6, 33, 33, 62, 62, 62, 62, 62, 62, 62, 62, 62, 2, 2, 2, 6, 6, 14, 14, 6, 14, 14, 1, 6, 6, 62, 62, 62] 201
rigid atoms, others: [0, 1, 2, 3, 36, 10, 11, 12, 13] set([4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037020 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037020/1 /scratch/stefan/7769618/working/building/REAL300000037020 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/21
`/scratch/stefan/7769618/working/3D/21' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(CC2=CC=CC=C2)=CN=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037020.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037020/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 35, 35, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 16, 35, 108, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 430
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [68, 68, 68, 68, 161, 201, 201, 161, 201, 201, 68, 68, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 68, 161, 161, 201, 201, 161, 201, 201, 68, 44, 10, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 673
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037020 none CN1C(CC2=CC=CC=C2)=CN=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 8, 16, 16, 8, 16, 16, 1, 1, 1, 1, 4, 4, 21, 68, 68, 68, 68, 68, 68, 76, 76, 68, 2, 2, 2, 8, 8, 16, 16, 8, 16, 16, 1, 4, 21, 68, 68, 68] 201
rigid atoms, others: [0, 1, 2, 3, 36, 10, 11, 12, 13] set([4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037020 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037020
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037020/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037020/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037020
Building REAL300000037021
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037021'
/scratch/stefan/7769618/working/building/REAL300000037021 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037021

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037021/0 /scratch/stefan/7769618/working/building/REAL300000037021 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/22
`/scratch/stefan/7769618/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CN=C(Cl)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037021 none NC1=CN=C(Cl)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 110, 111, 111, 111, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 111, 111, 111, 111, 60, 12, 1, 1, 1] 111
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037021 none NC1=CN=C(Cl)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 67, 111, 111, 111, 111, 111, 111, 111, 111, 111, 2, 2, 1, 1, 13, 67, 111, 111, 111] 111
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037021 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037021
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037021/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037021
Building REAL300000037022
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037022'
/scratch/stefan/7769618/working/building/REAL300000037022 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037022

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037022/0 /scratch/stefan/7769618/working/building/REAL300000037022 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/23
`/scratch/stefan/7769618/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1CC2=CC=CC=C2C1)

`REAL300000037022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037022 none CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1CC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 1, 5, 27, 27, 72, 72, 72, 72, 72, 72, 82, 82, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 5, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 82
rigid atoms, others: [33, 2, 35, 36, 37, 38, 39, 40, 41, 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: 173
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: REAL300000037022 none CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1CC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [47, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 72, 72, 72, 72, 72, 72, 72, 72, 59, 59, 59, 59, 59, 40, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72] 82
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 12, 13, 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: 415
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037022 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037022
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037022/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037022
Building REAL300000037023
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037023'
/scratch/stefan/7769618/working/building/REAL300000037023 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037023

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037023/0 /scratch/stefan/7769618/working/building/REAL300000037023 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/24
`/scratch/stefan/7769618/working/3D/24' -> `0.mol2'
Preparing input files

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

`REAL300000037023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037023 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 98, 98, 191, 191, 191, 191, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 191, 191, 191, 2, 2, 2, 1] 191
rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 302
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037023 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 191, 191, 191, 191, 191, 191, 191, 191, 191, 50, 50, 50, 50, 1, 1, 1, 191, 191, 191, 191] 191
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037023 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037023/1 /scratch/stefan/7769618/working/building/REAL300000037023 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/25
`/scratch/stefan/7769618/working/3D/25' -> `1.mol2'
Preparing input files

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

`REAL300000037023.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037023/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037023 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 10, 10, 24, 44, 44, 44, 2, 2, 2, 1] 44
rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 104
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037023 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [29, 30, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 30, 30, 11, 1, 1, 1, 44, 44, 44, 44] 44
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 82
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037023 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037023
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037023/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037023/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037023
Building REAL300000037024
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037024'
/scratch/stefan/7769618/working/building/REAL300000037024 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037024

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037024/0 /scratch/stefan/7769618/working/building/REAL300000037024 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/26
`/scratch/stefan/7769618/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CP(C)(=O)C1CCCC(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C1)

`REAL300000037024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037024 none CP(C)(=O)C1CCCC(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'P.3', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 13, 5, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 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, 38, 77, 77, 38, 38, 38, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 77, 77, 77, 77, 77, 77, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 38, 38] 77
rigid atoms, others: [36, 37, 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, 35, 39, 40])
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: REAL300000037024 none CP(C)(=O)C1CCCC(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'P.3', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 13, 5, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 38, 38, 46, 46, 38, 1, 10, 10, 10, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 1, 1] 77
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 7, 8, 9, 39, 40, 21, 33, 28, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 36, 37, 38])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037024 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037024
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037024/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037024
Building REAL300000037025
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037025'
/scratch/stefan/7769618/working/building/REAL300000037025 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037025

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037025/0 /scratch/stefan/7769618/working/building/REAL300000037025 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/27
`/scratch/stefan/7769618/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl)

`REAL300000037025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 70, 56, 56, 19, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 56, 56, 56, 56, 56, 19, 4, 12, 12, 12, 12, 1, 1, 56, 56] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 217
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 201, 169, 169, 98, 30, 30, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 169, 169, 169, 169, 169, 98, 30, 1, 1, 1, 1, 12, 12, 169, 169] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 485
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 10, 40, 40, 56, 56, 56, 169, 169, 169, 169, 169, 201, 201, 169, 56, 56, 1, 1, 1, 1, 1, 10, 40, 169, 169, 169, 169, 56, 56, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 527
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037025 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037025/1 /scratch/stefan/7769618/working/building/REAL300000037025 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/28
`/scratch/stefan/7769618/working/3D/28' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl)

`REAL300000037025.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037025/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 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, 2, 2, 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: [26, 26, 26, 26, 26, 22, 22, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 6, 1, 1, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 1, 1, 26, 26] 30
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 6, 6, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 6, 6, 30, 30] 30
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 72
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037025 none O=C([O-])C1=CC(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 20, 26, 26, 26, 30, 30, 30, 30, 30, 30, 30, 30, 26, 26, 1, 1, 1, 1, 1, 20, 20, 30, 30, 30, 30, 26, 26, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037025 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037025
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037025/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037025/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037025
Building REAL300000037026
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037026'
/scratch/stefan/7769618/working/building/REAL300000037026 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037026

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037026/0 /scratch/stefan/7769618/working/building/REAL300000037026 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/29
`/scratch/stefan/7769618/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC(F)=C2F)=CC=C1Cl)

`REAL300000037026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037026 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC(F)=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 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]
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, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 9, 1, 1, 50, 50] 50
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 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: REAL300000037026 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC(F)=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 13, 39, 50, 50, 1, 1] 50
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 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/7769618/working/building/REAL300000037026 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037026
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037026/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037026
Building REAL300000037027
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037027'
/scratch/stefan/7769618/working/building/REAL300000037027 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037027

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037027/0 /scratch/stefan/7769618/working/building/REAL300000037027 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/30
`/scratch/stefan/7769618/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1C1=CC=CN=C1)

`REAL300000037027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037027 none CC1(C)C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 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, 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]
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: [21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 21, 21, 40, 40, 40, 40, 40, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 21, 21, 21, 40, 40, 40, 40] 40
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 15, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 85
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037027 none CC1(C)C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 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, 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]
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: [5, 5, 5, 5, 5, 17, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 5, 5, 5, 1, 1, 1, 1] 40
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 60
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037027 none CC1(C)C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 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, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5] 40
rigid atoms, others: [0, 1, 2, 3, 4, 34, 16, 17, 18, 35, 36, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 45
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037027 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037027
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037027/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037027
Building REAL300000037028
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037028'
/scratch/stefan/7769618/working/building/REAL300000037028 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037028

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037028/0 /scratch/stefan/7769618/working/building/REAL300000037028 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/31
`/scratch/stefan/7769618/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC3=C2CCCC3)=CC=C1Cl)

`REAL300000037028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037028 none O=C([O-])C1=CC(NN=CC2=CC=CC3=C2CCCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 82, 82, 49, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82] 82
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 38, 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: REAL300000037028 none O=C([O-])C1=CC(NN=CC2=CC=CC3=C2CCCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 47, 47, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 13, 47, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1] 82
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037028 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037028
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037028/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037028
Building REAL300000037029
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037029'
/scratch/stefan/7769618/working/building/REAL300000037029 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037029

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037029/0 /scratch/stefan/7769618/working/building/REAL300000037029 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/32
`/scratch/stefan/7769618/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)=CC=C1Cl)

`REAL300000037029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037029 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 69, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 125, 125, 126, 69, 12, 1, 1, 1, 126, 126] 126
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30])
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: REAL300000037029 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 56, 56, 126, 126, 126, 103, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 13, 56, 126, 118, 126, 1, 1] 126
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])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037029 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037029
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037029/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037029
Building REAL300000037030
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037030'
/scratch/stefan/7769618/working/building/REAL300000037030 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037030

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037030/0 /scratch/stefan/7769618/working/building/REAL300000037030 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/33
`/scratch/stefan/7769618/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1)

`REAL300000037030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037030 none CC1=CN=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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
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, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 99, 99, 99, 99, 99, 99, 99, 50, 13, 1, 1, 1, 99, 99, 99, 99] 99
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037030 none CC1=CN=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 62, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 2, 2, 2, 1, 12, 62, 99, 99, 99, 2, 2, 2, 1] 99
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 216
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037030 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037030
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037030/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037030
Building REAL300000037031
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037031'
/scratch/stefan/7769618/working/building/REAL300000037031 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037031

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037031/0 /scratch/stefan/7769618/working/building/REAL300000037031 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/34
`/scratch/stefan/7769618/working/3D/34' -> `0.mol2'
Preparing input files

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

`REAL300000037031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037031 none CC(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [90, 84, 90, 84, 84, 84, 84, 94, 94, 94, 84, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 90, 90, 90, 90, 90, 90, 90, 94, 94, 94, 94, 94, 94, 94, 94, 94, 84, 44, 8, 1, 1, 1] 99
rigid atoms, others: [46, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 220
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037031 none CC(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [2, 1, 2, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 11, 43, 84, 84, 84, 84, 84, 84, 93, 93, 84, 3, 3, 3, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 11, 43, 84, 84, 84] 98
rigid atoms, others: [1, 3, 4, 5, 6, 41, 10, 11, 12] set([0, 2, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 228
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037031 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037031
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037031/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037031
Building REAL300000037032
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037032'
/scratch/stefan/7769618/working/building/REAL300000037032 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037032

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037032/0 /scratch/stefan/7769618/working/building/REAL300000037032 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/35
`/scratch/stefan/7769618/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2F)=CC=C1Cl)

`REAL300000037032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037032 none O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 52, 53, 52, 52, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 27, 8, 1, 1, 1, 52, 52] 53
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 30, 31])
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: REAL300000037032 none O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 52, 52, 46, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 10, 40, 52, 52, 52, 1, 1] 53
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037032 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037032
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037032/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037032
Building REAL300000037033
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037033'
/scratch/stefan/7769618/working/building/REAL300000037033 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037033

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037033/0 /scratch/stefan/7769618/working/building/REAL300000037033 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/36
`/scratch/stefan/7769618/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=N3)C=C2)=CC=C1Cl)

`REAL300000037033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037033 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=N3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 11, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 21, 21, 21, 21, 21, 11, 3, 1, 1, 2, 2, 1, 1, 21, 21] 37
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037033 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=N3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 22, 6, 6, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 37, 37, 37, 37, 37, 22, 6, 2, 2, 1, 1, 2, 2, 37, 37] 37
rigid atoms, others: [12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 89
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037033 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=N3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 21, 21, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 1, 1, 1, 1, 1, 9, 21, 21, 21, 37, 37, 21, 21, 1, 1] 37
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 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
/scratch/stefan/7769618/working/building/REAL300000037033 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037033
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037033/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037033
Building REAL300000037034
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037034'
/scratch/stefan/7769618/working/building/REAL300000037034 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037034

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037034/0 /scratch/stefan/7769618/working/building/REAL300000037034 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/37
`/scratch/stefan/7769618/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC2=CC=CC=C12)

`REAL300000037034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037034 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 44, 12, 1, 1, 1, 90, 90, 90, 90, 90, 90] 90
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 146
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: REAL300000037034 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 55, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 55, 90, 90, 90, 1, 1, 1, 1, 1, 1] 90
rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23, 37] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 188
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037034 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037034
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037034/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037034
Building REAL300000037035
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037035'
/scratch/stefan/7769618/working/building/REAL300000037035 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037035

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037035/0 /scratch/stefan/7769618/working/building/REAL300000037035 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/38
`/scratch/stefan/7769618/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037035 none COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 55, 55, 55, 55, 55, 55, 55, 55, 55, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 55, 55, 55, 55, 55, 37, 9, 1, 1, 1] 56
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037035 none COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 55, 55, 55, 55, 55, 55, 56, 56, 55, 2, 2, 2, 1, 1, 1, 1, 1, 9, 26, 55, 55, 55] 56
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 32, 34, 35, 36, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037035 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037035
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037035/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037035
Building REAL300000037036
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037036'
/scratch/stefan/7769618/working/building/REAL300000037036 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037036

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037036/0 /scratch/stefan/7769618/working/building/REAL300000037036 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/39
`/scratch/stefan/7769618/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NC2C[C@H]3CSC[C@H]3C2)=CC=C1Cl)

`REAL300000037036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037036 none O=C([O-])C1=CC(N=NC2C[C@H]3CSC[C@H]3C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 1, 1, 1, 16, 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]
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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 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: REAL300000037036 none O=C([O-])C1=CC(N=NC2C[C@H]3CSC[C@H]3C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 14, 5, 5, 7, 5, 1, 1, 1, 16, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037036 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037036
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037036/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037036
Building REAL300000037037
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037037'
/scratch/stefan/7769618/working/building/REAL300000037037 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037037

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037037/0 /scratch/stefan/7769618/working/building/REAL300000037037 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/40
`/scratch/stefan/7769618/working/3D/40' -> `0.mol2'
Preparing input files

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

`REAL300000037037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037037 none CC1(C)CC(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23] 23
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 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: 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: REAL300000037037 none CC1(C)CC(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CC1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 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, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 23, 23, 23, 1, 1, 2, 2, 2, 2, 2, 2] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037037 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037037
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037037/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037037
Building REAL300000037038
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037038'
/scratch/stefan/7769618/working/building/REAL300000037038 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037038

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037038/0 /scratch/stefan/7769618/working/building/REAL300000037038 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/41
`/scratch/stefan/7769618/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)S1)

`REAL300000037038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037038 none CC1=NC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 66, 67, 67, 67, 40, 12, 1, 1, 1, 67, 67, 67] 67
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, 28, 29, 30])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037038 none CC1=NC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 48, 67, 67, 67, 67, 67, 67, 67, 67, 66, 1, 1, 1, 2, 2, 2, 10, 48, 67, 67, 66, 1, 1, 1] 67
rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037038 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037038
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037038/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037038
Building REAL300000037039
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037039'
/scratch/stefan/7769618/working/building/REAL300000037039 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037039

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037039/0 /scratch/stefan/7769618/working/building/REAL300000037039 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/42
`/scratch/stefan/7769618/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3CCC(O)C3)C=C2)=CC=C1Cl)

`REAL300000037039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037039 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCC(O)C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 30, 16, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 30, 30, 30, 30, 30, 16, 3, 1, 1, 5, 5, 5, 5, 5, 15, 5, 5, 1, 1, 30, 30] 225
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 78
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037039 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCC(O)C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 43, 13, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 75, 75, 75, 75, 75, 43, 13, 5, 5, 1, 1, 1, 1, 1, 6, 1, 1, 5, 5, 75, 75] 225
rigid atoms, others: [32, 33, 34, 36, 37, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 38, 39, 40, 41])
total number of confs: 173
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037039 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCC(O)C3)C=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 29, 29, 30, 30, 29, 29, 75, 75, 75, 75, 75, 30, 30, 1, 1, 1, 1, 1, 11, 29, 30, 30, 75, 75, 75, 75, 75, 225, 75, 75, 30, 30, 1, 1] 225
rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 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, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 349
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037039 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037039
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037039/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037039
Building REAL300000037040
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037040'
/scratch/stefan/7769618/working/building/REAL300000037040 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037040

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037040/0 /scratch/stefan/7769618/working/building/REAL300000037040 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/43
`/scratch/stefan/7769618/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037040 none COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [158, 131, 131, 131, 131, 131, 131, 193, 130, 131, 181, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 158, 158, 158, 131, 131, 193, 193, 193, 181, 181, 181, 31, 9, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 444
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037040 none COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 1, 1, 13, 13, 61, 131, 131, 131, 131, 131, 131, 143, 143, 131, 4, 4, 4, 1, 1, 3, 3, 3, 6, 6, 6, 13, 61, 131, 131, 131] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 28, 29] set([0, 7, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037040 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037040
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037040/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037040
Building REAL300000037041
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037041'
/scratch/stefan/7769618/working/building/REAL300000037041 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037041

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037041/0 /scratch/stefan/7769618/working/building/REAL300000037041 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/44
`/scratch/stefan/7769618/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1N=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C)

`REAL300000037041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037041 none CCCN1N=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 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, 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: [201, 194, 98, 98, 98, 98, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 98, 98, 201, 201, 201, 201, 201, 194, 194, 98, 41, 10, 1, 1, 1, 98, 98, 98] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37])
total number of confs: 677
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037041 none CCCN1N=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 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, 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: [9, 5, 1, 1, 1, 1, 1, 1, 10, 10, 41, 98, 98, 98, 98, 98, 98, 104, 104, 98, 1, 1, 10, 10, 10, 9, 9, 5, 5, 1, 10, 41, 98, 98, 98, 2, 2, 2] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037041 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037041
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037041/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037041
Building REAL300000037042
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037042'
/scratch/stefan/7769618/working/building/REAL300000037042 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037042

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037042/0 /scratch/stefan/7769618/working/building/REAL300000037042 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/45
`/scratch/stefan/7769618/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)=CC=C1Cl)

`REAL300000037042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037042 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 84, 95, 84, 84, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 84, 84, 84, 84, 84, 39, 10, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 84, 84] 155
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, 43, 44, 45])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037042 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 155, 155, 118, 42, 42, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 118, 42, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155] 155
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45])
total number of confs: 368
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037042 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 35, 35, 84, 84, 84, 84, 84, 84, 154, 154, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 8, 35, 84, 84, 84, 84, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1] 155
rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037042 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037042
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037042/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037042
Building REAL300000037043
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037043'
/scratch/stefan/7769618/working/building/REAL300000037043 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037043

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037043/0 /scratch/stefan/7769618/working/building/REAL300000037043 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/46
`/scratch/stefan/7769618/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)=CC=C1Cl)

`REAL300000037043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037043 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 103, 103, 77, 103, 103, 103, 33, 33, 33, 33, 33, 18, 5, 1, 1, 1, 1, 30, 30, 103, 103, 103, 103, 33, 33] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037043 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 190, 133, 133, 103, 103, 103, 103, 103, 103, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 133, 103, 103, 103, 103, 8, 8, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 492
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037043 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 18, 18, 33, 33, 18, 33, 33, 33, 75, 157, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7, 18, 33, 33, 33, 33, 157, 157, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037043 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037043
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037043/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037043
Building REAL300000037044
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037044'
/scratch/stefan/7769618/working/building/REAL300000037044 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037044

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037044/0 /scratch/stefan/7769618/working/building/REAL300000037044 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/47
`/scratch/stefan/7769618/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=NC=CC=C2C=C1)

`REAL300000037044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037044 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 46, 11, 1, 1, 1, 85, 85, 85, 85, 85] 85
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 138
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037044 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 43, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 43, 85, 85, 85, 1, 1, 1, 1, 1] 85
rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 167
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037044 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037044
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037044/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037044
Building REAL300000037045
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037045'
/scratch/stefan/7769618/working/building/REAL300000037045 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037045

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037045/0 /scratch/stefan/7769618/working/building/REAL300000037045 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/48
`/scratch/stefan/7769618/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2F)=CC=C1Cl)

`REAL300000037045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037045 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
1  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 51, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 51, 13, 2, 1, 1, 1, 67, 67] 134
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, 29])
total number of confs: 157
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: REAL300000037045 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
1  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 35, 35, 67, 67, 67, 48, 67, 67, 67, 1, 1, 1, 1, 1, 10, 35, 134, 67, 66, 67, 1, 1] 134
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27])
total number of confs: 317
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037045 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037045/1 /scratch/stefan/7769618/working/building/REAL300000037045 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/49
`/scratch/stefan/7769618/working/3D/49' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=C([O-])C=CC=C2F)=CC=C1Cl)

`REAL300000037045.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037045/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037045 none O=C([O-])C1=CC(NN=CC2=C([O-])C=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 10, 4, 1, 1, 1, 13, 13] 13
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: 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: REAL300000037045 none O=C([O-])C1=CC(NN=CC2=C([O-])C=CC=C2F)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 4, 10, 10, 13, 13, 13, 11, 13, 13, 13, 1, 1, 1, 1, 1, 4, 10, 13, 13, 13, 1, 1] 13
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])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037045 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037045
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037045/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037045/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037045
Building REAL300000037046
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037046'
/scratch/stefan/7769618/working/building/REAL300000037046 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037046

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037046/0 /scratch/stefan/7769618/working/building/REAL300000037046 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/50
`/scratch/stefan/7769618/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CN=C1N1C=CC=N1)

`REAL300000037046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037046 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CN=C1N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 1, 8, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 82, 83, 83, 83, 83, 83, 83, 83, 82, 48, 12, 1, 1, 1, 82, 83, 83, 83] 83
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037046 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CN=C1N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 1, 8, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 57, 83, 83, 83, 83, 83, 83, 83, 83, 83, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 57, 83, 83, 83, 4, 1, 1, 1] 83
rigid atoms, others: [35, 36, 37, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 179
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037046 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CN=C1N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 1, 8, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 54, 82, 82, 82, 82, 82, 82, 83, 83, 82, 1, 1, 1, 1, 4, 4, 4, 4, 2, 2, 2, 1, 10, 54, 82, 82, 82, 1, 4, 4, 4] 83
rigid atoms, others: [0, 1, 2, 3, 4, 34, 17, 18, 19, 20, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037046 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037046
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037046/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037046
Building REAL300000037047
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037047'
/scratch/stefan/7769618/working/building/REAL300000037047 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037047

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037047/0 /scratch/stefan/7769618/working/building/REAL300000037047 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/51
`/scratch/stefan/7769618/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1)

`REAL300000037047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037047 none COC(=O)C1=CN(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 83, 151, 83, 83, 83, 83, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 83, 151, 151, 151, 83, 84, 84, 84, 36, 8, 1, 1, 1, 83] 151
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 378
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037047 none COC(=O)C1=CN(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 12, 12, 48, 83, 83, 83, 83, 83, 83, 89, 89, 83, 1, 13, 13, 13, 1, 2, 2, 2, 12, 48, 83, 83, 83, 1] 151
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 22, 26] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037047 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037047
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037047/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037047
Building REAL300000037048
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037048'
/scratch/stefan/7769618/working/building/REAL300000037048 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037048

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037048/0 /scratch/stefan/7769618/working/building/REAL300000037048 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/52
`/scratch/stefan/7769618/working/3D/52' -> `0.mol2'
Preparing input files

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

`REAL300000037048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037048 none COC1=CN=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 162, 162, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 162, 201, 201, 201, 162, 162, 53, 53, 53, 10, 1, 1, 1, 162] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 305
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: REAL300000037048 none COC1=CN=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 12, 69, 162, 162, 162, 162, 162, 162, 177, 177, 162, 1, 2, 2, 2, 1, 1, 13, 13, 13, 68, 162, 162, 162, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 368
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037048 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037048
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037048/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037048
Building REAL300000037049
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037049'
/scratch/stefan/7769618/working/building/REAL300000037049 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037049

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037049/0 /scratch/stefan/7769618/working/building/REAL300000037049 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/53
`/scratch/stefan/7769618/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(C=C(Cl)S3)N2)=CC=C1Cl)

`REAL300000037049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037049 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C(Cl)S3)N2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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, 46, 47, 46, 46, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 47, 47, 47, 46, 26, 6, 1, 1, 1, 46, 47] 47
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 28, 29])
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: REAL300000037049 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C(Cl)S3)N2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 38, 38, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 10, 38, 46, 46, 46, 1, 1] 47
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037049 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037049
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037049/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037049
Building REAL300000037050
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037050'
/scratch/stefan/7769618/working/building/REAL300000037050 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037050

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037050/0 /scratch/stefan/7769618/working/building/REAL300000037050 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/54
`/scratch/stefan/7769618/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NC2CCC2CC2=CC=CC=C2)=CC=C1Cl)

`REAL300000037050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037050 none O=C([O-])C1=CC(N=NC2CCC2CC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [69, 46, 69, 46, 46, 13, 13, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 8, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 7, 8, 8, 46, 46] 120
rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037050 none O=C([O-])C1=CC(N=NC2CCC2CC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 69, 69, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 120, 120] 120
rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 183
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037050 none O=C([O-])C1=CC(N=NC2CCC2CC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 99, 120, 120, 116, 120, 120, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 99, 99, 120, 120, 111, 120, 120, 1, 1] 120
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037050 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037050
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037050/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037050
Building REAL300000037051
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037051'
/scratch/stefan/7769618/working/building/REAL300000037051 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037051

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037051/0 /scratch/stefan/7769618/working/building/REAL300000037051 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/55
`/scratch/stefan/7769618/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1)

`REAL300000037051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037051 none COC1=CC2=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 128, 128, 128, 128, 64, 64, 63, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 128, 128, 128, 128, 128, 128, 138, 138, 138, 128, 64, 64, 64, 13, 1, 1, 1, 128, 128, 128, 128] 138
rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 220
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037051 none COC1=CC2=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 9, 38, 128, 128, 128, 128, 128, 128, 138, 138, 128, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 9, 9, 9, 38, 128, 128, 128, 1, 1, 1, 1] 138
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24, 25, 38, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 259
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037051 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037051/1 /scratch/stefan/7769618/working/building/REAL300000037051 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/56
`/scratch/stefan/7769618/working/3D/56' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C(C)N=NC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1)

`REAL300000037051.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037051/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037051 none COC1=CC2=C(C(C)N=NC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 81, 81, 81, 81, 40, 9, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 81, 81, 81, 81, 81, 81, 89, 89, 89, 81, 40, 40, 40, 40, 1, 1, 1, 81, 81, 81, 81] 89
rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 212
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: REAL300000037051 none COC1=CC2=C(C(C)N=NC3=CC=C(Cl)C(C(=O)[O-])=C3)N=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 81, 81, 81, 81, 81, 81, 89, 89, 81, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 5, 5, 5, 5, 81, 81, 81, 1, 1, 1, 1] 89
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24, 25, 38, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 160
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037051 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037051
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037051/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037051/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037051
Building REAL300000037052
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037052'
/scratch/stefan/7769618/working/building/REAL300000037052 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037052

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037052/0 /scratch/stefan/7769618/working/building/REAL300000037052 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/57
`/scratch/stefan/7769618/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=NC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N2C=C1)

`REAL300000037052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037052 none COC1=CC2=NC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [176, 158, 158, 158, 157, 157, 157, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 157, 158, 158, 176, 176, 176, 158, 157, 66, 12, 1, 1, 1, 158, 158] 176
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 270
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037052 none COC1=CC2=NC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 75, 158, 158, 158, 158, 158, 158, 176, 176, 158, 1, 1, 1, 3, 3, 3, 1, 1, 12, 74, 158, 158, 158, 1, 1] 176
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037052 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037052
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037052/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037052
Building REAL300000037053
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037053'
/scratch/stefan/7769618/working/building/REAL300000037053 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037053

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037053/0 /scratch/stefan/7769618/working/building/REAL300000037053 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/58
`/scratch/stefan/7769618/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C2CCCN2N=C1)

`REAL300000037053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037053 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C2CCCN2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 57, 98, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1] 98
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] 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: 197
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037053 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C2CCCN2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 98, 98, 98, 98, 98, 98, 98, 45, 45, 45, 11, 1, 1, 1, 98, 98, 98, 98, 98, 98, 98] 98
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 161
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037053 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037053
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037053/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037053
Building REAL300000037054
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037054'
/scratch/stefan/7769618/working/building/REAL300000037054 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037054

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037054/0 /scratch/stefan/7769618/working/building/REAL300000037054 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/59
`/scratch/stefan/7769618/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O)

`REAL300000037054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037054 none COC1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [183, 167, 167, 167, 167, 167, 167, 61, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 167, 167, 183, 183, 183, 167, 167, 61, 11, 1, 1, 1, 334] 366
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 602
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: REAL300000037054 none COC1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 72, 167, 167, 167, 167, 167, 167, 183, 183, 167, 1, 1, 3, 3, 3, 1, 1, 12, 72, 167, 167, 167, 2] 366
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 368
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037054 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037054
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037054/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037054
Building REAL300000037055
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037055'
/scratch/stefan/7769618/working/building/REAL300000037055 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037055

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037055/0 /scratch/stefan/7769618/working/building/REAL300000037055 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/60
`/scratch/stefan/7769618/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)=CC=C1Cl)

`REAL300000037055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037055 none O=C([O-])C1=CC(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 6, 19, 51, 84, 84, 57, 84, 84, 1, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 51, 51, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [32, 43, 7, 8, 9, 10, 11, 44, 45, 46, 47, 42, 20, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49])
total number of confs: 367
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037055 none O=C([O-])C1=CC(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 168, 168, 84, 84, 84, 47, 13, 3, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 201, 201, 201, 201, 201, 84, 84, 84, 84, 47, 47, 3, 3, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 487
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037055 none O=C([O-])C1=CC(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 16, 16, 16, 45, 108, 201, 201, 201, 201, 201, 201, 16, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 16, 16, 45, 45, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 48, 49, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 689
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037055 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037055
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037055/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037055
Building REAL300000037056
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037056'
/scratch/stefan/7769618/working/building/REAL300000037056 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037056

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037056/0 /scratch/stefan/7769618/working/building/REAL300000037056 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/61
`/scratch/stefan/7769618/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1N=C(C)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037056 none CCCN1N=C(C)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 189, 123, 123, 123, 123, 123, 123, 44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 189, 189, 123, 123, 123, 123, 44, 9, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 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])
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: REAL300000037056 none CCCN1N=C(C)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 123, 123, 122, 122, 123, 123, 132, 132, 123, 12, 12, 12, 12, 12, 6, 6, 2, 2, 2, 1, 10, 56, 123, 123, 123] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037056 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037056
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037056/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037056
Building REAL300000037057
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037057'
/scratch/stefan/7769618/working/building/REAL300000037057 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037057

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037057/0 /scratch/stefan/7769618/working/building/REAL300000037057 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/62
`/scratch/stefan/7769618/working/3D/62' -> `0.mol2'
Preparing input files

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

`REAL300000037057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037057 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 1, 13, 13, 51, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 51, 90, 90, 90, 1, 1] 90
rigid atoms, others: [1, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037057 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 90, 90, 90, 90, 90, 90, 90, 90, 45, 45, 45, 10, 1, 1, 1, 90, 90] 90
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 143
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037057 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037057
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037057/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037057
Building REAL300000037058
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037058'
/scratch/stefan/7769618/working/building/REAL300000037058 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037058

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037058/0 /scratch/stefan/7769618/working/building/REAL300000037058 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/63
`/scratch/stefan/7769618/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2CCC2)=N1)

`REAL300000037058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037058 none CN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2CCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 109, 109, 150, 150, 150, 109, 109, 109, 109, 109, 45, 9, 1, 1, 1, 150, 150, 150, 150, 150, 150, 150] 150
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 316
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037058 none CN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2CCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 42, 42, 116, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 42, 116, 150, 150, 150, 1, 1, 1, 1, 1, 1, 1] 150
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 344
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037058 none CN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2CCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
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, 10, 10, 56, 109, 109, 109, 109, 109, 109, 117, 117, 109, 1, 1, 9, 9, 9, 1, 2, 2, 2, 1, 10, 56, 109, 109, 109, 9, 9, 9, 9, 9, 9, 9] 150
rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037058 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037058
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037058/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037058
Building REAL300000037059
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037059'
/scratch/stefan/7769618/working/building/REAL300000037059 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037059

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037059/0 /scratch/stefan/7769618/working/building/REAL300000037059 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/64
`/scratch/stefan/7769618/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)

`REAL300000037059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037059 none CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [47, 9, 47, 91, 145, 145, 145, 145, 145, 145, 145, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 47, 47, 91, 91, 145, 145, 145, 1, 1, 1] 145
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 465
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037059 none CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 84, 84, 145, 145, 145, 145, 145, 145, 145, 145, 145, 16, 16, 16, 16, 8, 8, 1, 1, 1, 145, 145, 145] 145
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 245
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037059 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037059
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037059/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037059
Building REAL300000037060
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037060'
/scratch/stefan/7769618/working/building/REAL300000037060 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037060

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037060/0 /scratch/stefan/7769618/working/building/REAL300000037060 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/65
`/scratch/stefan/7769618/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)O1)

`REAL300000037060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037060 none CC(C)(C)C1=NC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [124, 80, 124, 124, 79, 80, 80, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 80, 124, 124, 124, 124, 124, 124, 124, 124, 124, 80, 49, 12, 1, 1, 1] 124
rigid atoms, others: [34, 35, 36, 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])
total number of confs: 388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037060 none CC(C)(C)C1=NC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 42, 81, 81, 81, 81, 81, 81, 90, 90, 80, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 41, 81, 81, 80] 124
rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037060 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037060
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037060/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037060
Building REAL300000037061
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037061'
/scratch/stefan/7769618/working/building/REAL300000037061 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037061

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037061/0 /scratch/stefan/7769618/working/building/REAL300000037061 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/66
`/scratch/stefan/7769618/working/3D/66' -> `0.mol2'
Preparing input files

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

`REAL300000037061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037061 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 56, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11, 56, 110, 110, 110, 1, 1, 1] 110
rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 220
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037061 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [54, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 110, 110, 89, 110, 110, 110, 110, 110, 110, 110, 55, 55, 55, 13, 1, 1, 1, 110, 110, 110] 110
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 256
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037061 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037061
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037061/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037061
Building REAL300000037062
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037062'
/scratch/stefan/7769618/working/building/REAL300000037062 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037062

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037062/0 /scratch/stefan/7769618/working/building/REAL300000037062 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/67
`/scratch/stefan/7769618/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1Cl)

`REAL300000037062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037062 none CC1=CC=C(NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [88, 44, 88, 88, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 39, 70, 70, 88, 88, 88, 88, 88, 88, 88, 88, 23, 6, 1, 1, 1, 1, 39, 39, 88] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 522
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037062 none CC1=CC=C(NN=CC2=CC=CC=C2OCC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 45, 88, 88, 45, 88, 88, 88, 160, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 11, 45, 88, 88, 88, 88, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037062 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037062
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037062/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037062
Building REAL300000037063
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037063'
/scratch/stefan/7769618/working/building/REAL300000037063 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037063

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037063/0 /scratch/stefan/7769618/working/building/REAL300000037063 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/68
`/scratch/stefan/7769618/working/3D/68' -> `0.mol2'
Preparing input files

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

`REAL300000037063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037063 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 34, 127, 127, 89, 127, 127, 127, 127, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 34, 127, 127, 127, 127, 127, 127, 1, 1, 12, 12, 1, 1] 194
rigid atoms, others: [1, 36, 37, 40, 41, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 365
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037063 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [25, 2, 25, 48, 122, 194, 194, 193, 193, 194, 194, 194, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 26, 122, 194, 194, 194, 194, 194, 194, 12, 12, 1, 1, 12, 12] 194
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, 40, 41])
total number of confs: 469
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037063 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 127, 127, 65, 97, 194, 194, 194, 194, 194, 194, 194, 127, 127, 59, 59, 59, 11, 1, 1, 2, 2, 2, 1, 127, 127, 194, 194, 127, 127] 194
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 555
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037063 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037063
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037063/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037063
Building REAL300000037064
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037064'
/scratch/stefan/7769618/working/building/REAL300000037064 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037064

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037064/0 /scratch/stefan/7769618/working/building/REAL300000037064 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/69
`/scratch/stefan/7769618/working/3D/69' -> `0.mol2'
Preparing input files

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

`REAL300000037064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037064 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 51, 51, 51, 19, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 142, 198, 201, 201, 84, 84, 84, 51, 18, 6, 1, 1, 2, 2, 2, 1, 51, 51, 198, 198] 201
rigid atoms, others: [35, 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, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037064 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 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, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 9, 37, 57, 57, 3, 3, 3, 1, 7, 17, 51, 51, 51, 51, 51, 51, 1, 1, 37, 37] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037064 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037064
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037064/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037064
Building REAL300000037065
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037065'
/scratch/stefan/7769618/working/building/REAL300000037065 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037065

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037065/0 /scratch/stefan/7769618/working/building/REAL300000037065 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/70
`/scratch/stefan/7769618/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl)

`REAL300000037065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037065 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [61, 33, 61, 61, 16, 4, 4, 1, 1, 1, 1, 1, 1, 6, 26, 50, 50, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 16, 4, 1, 1, 26, 26, 1, 1, 61] 201
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35])
total number of confs: 355
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: REAL300000037065 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 40, 40, 61, 61, 40, 40, 142, 201, 201, 201, 61, 61, 1, 1, 1, 2, 2, 2, 1, 1, 10, 40, 61, 61, 201, 201, 61, 61, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 608
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037065 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037065
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037065/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037065
Building REAL300000037066
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037066'
/scratch/stefan/7769618/working/building/REAL300000037066 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037066

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037066/0 /scratch/stefan/7769618/working/building/REAL300000037066 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/71
`/scratch/stefan/7769618/working/3D/71' -> `0.mol2'
Preparing input files

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

`REAL300000037066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037066 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 19, 65, 65, 36, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 7, 21, 33, 33, 1, 9, 9, 9, 19, 65, 65, 65, 65, 65, 65, 1, 1, 1, 21, 21, 1] 201
rigid atoms, others: [1, 34, 35, 38, 33, 12, 13, 14, 15, 16, 17, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 321
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: REAL300000037066 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 65, 65, 65, 65, 65, 139, 201, 201, 201, 65, 27, 27, 27, 6, 1, 1, 2, 2, 2, 1, 65, 65, 65, 201, 201, 65] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 543
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037066 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037066
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037066/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037066
Building REAL300000037067
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037067'
/scratch/stefan/7769618/working/building/REAL300000037067 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037067

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037067/0 /scratch/stefan/7769618/working/building/REAL300000037067 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/72
`/scratch/stefan/7769618/working/3D/72' -> `0.mol2'
Preparing input files

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

`REAL300000037067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037067 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 22, 70, 70, 36, 70, 70, 70, 70, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 22, 70, 70, 70, 70, 70, 70, 1, 1, 9, 17, 17, 1, 1] 165
rigid atoms, others: [1, 36, 37, 41, 42, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 317
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037067 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 70, 70, 22, 22, 104, 104, 104, 147, 165, 165, 165, 70, 70, 23, 23, 23, 6, 1, 1, 2, 2, 2, 1, 70, 70, 147, 165, 165, 70, 70] 165
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 789
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037067 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037067
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037067/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037067
Building REAL300000037068
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037068'
/scratch/stefan/7769618/working/building/REAL300000037068 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037068

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037068/0 /scratch/stefan/7769618/working/building/REAL300000037068 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/73
`/scratch/stefan/7769618/working/3D/73' -> `0.mol2'
Preparing input files

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

`REAL300000037068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037068 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 25, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1] 44
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037068 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 44, 44, 35, 35, 44, 44, 44, 44, 36, 36, 36, 11, 1, 1, 2, 2, 2, 1, 44, 44, 44, 44] 44
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 145
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037068 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037068
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037068/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037068
Building REAL300000037069
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037069'
/scratch/stefan/7769618/working/building/REAL300000037069 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037069

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037069/0 /scratch/stefan/7769618/working/building/REAL300000037069 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/74
`/scratch/stefan/7769618/working/3D/74' -> `0.mol2'
Preparing input files

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

`REAL300000037069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037069 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 73, 73, 68, 73, 73, 73, 73, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 30, 73, 73, 73, 73, 73, 73, 1, 1, 2, 2, 1, 1] 105
rigid atoms, others: [32, 1, 36, 37, 33, 12, 13, 14, 15, 16, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 181
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037069 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 73, 73, 47, 51, 105, 105, 105, 73, 73, 48, 48, 48, 12, 1, 1, 2, 2, 2, 1, 73, 73, 105, 105, 73, 73] 105
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 452
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037069 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037069
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037069/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037069
Building REAL300000037070
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037070'
/scratch/stefan/7769618/working/building/REAL300000037070 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037070

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037070/0 /scratch/stefan/7769618/working/building/REAL300000037070 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/75
`/scratch/stefan/7769618/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl)

`REAL300000037070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037070 none CC1=CC=C(NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 50, 50, 15, 4, 4, 1, 1, 1, 1, 1, 1, 6, 22, 37, 52, 44, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 15, 4, 1, 1, 22, 22, 37, 37, 1, 1, 50] 201
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38])
total number of confs: 357
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: REAL300000037070 none CC1=CC=C(NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 31, 31, 50, 50, 31, 31, 115, 168, 201, 201, 197, 50, 50, 1, 1, 1, 2, 2, 2, 1, 1, 8, 31, 50, 50, 168, 168, 201, 201, 50, 50, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 709
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037070 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037070
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037070/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037070
Building REAL300000037071
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037071'
/scratch/stefan/7769618/working/building/REAL300000037071 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037071

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037071/0 /scratch/stefan/7769618/working/building/REAL300000037071 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/76
`/scratch/stefan/7769618/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1Cl)

`REAL300000037071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037071 none CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 16, 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, 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, 87, 87, 87, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 73, 73, 87, 87, 87, 87, 87, 87, 87, 87, 23, 5, 1, 1, 1, 42, 42, 87] 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, 35])
total number of confs: 371
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037071 none CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 16, 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, 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, 11, 47, 47, 87, 87, 87, 48, 87, 87, 87, 154, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 11, 47, 87, 87, 87, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 655
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037071 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037071
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037071/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037071
Building REAL300000037072
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037072'
/scratch/stefan/7769618/working/building/REAL300000037072 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037072

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037072/0 /scratch/stefan/7769618/working/building/REAL300000037072 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/77
`/scratch/stefan/7769618/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1Cl)

`REAL300000037072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037072 none CC1=CC=C(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens 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, 32, 57, 57, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 28, 28, 40, 40, 1, 57, 57, 57, 57, 57, 57, 57, 57, 19, 6, 1, 1, 1, 28, 28, 28, 28, 1, 57] 201
rigid atoms, others: [32, 37, 7, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38])
total number of confs: 330
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: REAL300000037072 none CC1=CC=C(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 8, 28, 28, 57, 57, 57, 57, 57, 153, 201, 201, 201, 201, 57, 1, 1, 1, 2, 2, 2, 1, 1, 8, 28, 57, 57, 57, 201, 201, 201, 201, 57, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 484
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037072 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037072
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037072/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037072
Building REAL300000037073
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037073'
/scratch/stefan/7769618/working/building/REAL300000037073 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037073

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037073/0 /scratch/stefan/7769618/working/building/REAL300000037073 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/78
`/scratch/stefan/7769618/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1Cl)

`REAL300000037073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037073 none CC1=CC=C(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens 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, 29, 55, 55, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 23, 31, 46, 39, 1, 55, 55, 55, 55, 55, 55, 55, 55, 15, 6, 1, 1, 1, 23, 23, 31, 31, 1, 55] 201
rigid atoms, others: [32, 37, 7, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38])
total number of confs: 361
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: REAL300000037073 none CC1=CC=C(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 20, 20, 55, 55, 55, 55, 55, 134, 177, 201, 201, 194, 55, 1, 1, 1, 2, 2, 2, 1, 1, 7, 20, 55, 55, 55, 177, 177, 201, 201, 55, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 549
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037073 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037073
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037073/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037073
Building REAL300000037074
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037074'
/scratch/stefan/7769618/working/building/REAL300000037074 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037074

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037074/0 /scratch/stefan/7769618/working/building/REAL300000037074 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/79
`/scratch/stefan/7769618/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1Cl)

`REAL300000037074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037074 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [69, 40, 70, 70, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 7, 19, 19, 19, 19, 19, 19, 21, 21, 1, 70, 70, 70, 70, 70, 70, 70, 70, 22, 6, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 70] 197
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, 45])
total number of confs: 273
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037074 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [197, 158, 197, 197, 101, 53, 53, 19, 19, 18, 19, 19, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 197, 197, 197, 197, 197, 197, 197, 197, 101, 53, 18, 19, 19, 5, 5, 1, 1, 1, 1, 19, 197] 197
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, 45])
total number of confs: 580
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037074 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 35, 35, 70, 70, 70, 70, 70, 107, 125, 197, 197, 197, 197, 197, 197, 197, 197, 70, 1, 1, 1, 2, 2, 2, 1, 1, 11, 35, 70, 70, 70, 125, 125, 197, 197, 197, 197, 70, 1] 197
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 385
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037074 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037074
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037074/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037074
Building REAL300000037075
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037075'
/scratch/stefan/7769618/working/building/REAL300000037075 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037075

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037075/0 /scratch/stefan/7769618/working/building/REAL300000037075 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/80
`/scratch/stefan/7769618/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1Cl)

`REAL300000037075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037075 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [26, 25, 26, 26, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 26, 26, 26, 27, 27, 27, 26, 26, 14, 6, 1, 1, 5, 5, 1, 26] 35
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, 37])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037075 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 16, 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, 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]
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, 6, 12, 12, 26, 26, 12, 12, 35, 35, 35, 35, 26, 26, 27, 27, 26, 1, 1, 1, 2, 2, 2, 1, 1, 6, 12, 26, 26, 35, 35, 26, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037075 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037075
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037075/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037075
Building REAL300000037076
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037076'
/scratch/stefan/7769618/working/building/REAL300000037076 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037076

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037076/0 /scratch/stefan/7769618/working/building/REAL300000037076 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/81
`/scratch/stefan/7769618/working/3D/81' -> `0.mol2'
Preparing input files

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

`REAL300000037076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037076 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 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, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 19, 19, 11, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 75, 75, 75, 75, 75, 75, 75, 1, 1, 11, 11, 11, 11, 3, 3, 1, 1, 7, 27, 75, 75, 75, 75, 75, 75, 1, 1, 11] 201
rigid atoms, others: [33, 34, 43, 8, 9, 10, 11, 12, 13, 14, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 183
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037076 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 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, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 79, 75, 50, 50, 75, 75, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 79, 79, 75, 75, 30, 8, 1, 1, 2, 2, 2, 1, 75, 75, 201] 201
rigid atoms, others: [37, 38, 42, 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, 39, 40, 41, 43, 44, 45])
total number of confs: 422
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037076 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 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, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 11, 11, 11, 11, 45, 45, 98, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 2, 2, 2, 9, 9, 11, 11, 45, 98, 201, 201, 201, 201, 201, 201, 10, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 426
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037076 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037076
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037076/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037076
Building REAL300000037077
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037077'
/scratch/stefan/7769618/working/building/REAL300000037077 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037077

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037077/0 /scratch/stefan/7769618/working/building/REAL300000037077 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/82
`/scratch/stefan/7769618/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1Cl)

`REAL300000037077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037077 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 31, 33, 33, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 3, 17, 17, 17, 17, 17, 18, 18, 17, 1, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 1, 1, 1, 3, 3, 17, 17, 17, 17, 1, 33] 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, 45])
total number of confs: 116
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037077 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [200, 200, 201, 201, 137, 78, 78, 17, 17, 17, 17, 17, 9, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 201, 201, 201, 201, 201, 201, 201, 201, 137, 78, 17, 17, 17, 8, 8, 1, 1, 1, 1, 17, 201] 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, 45])
total number of confs: 530
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037077 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [1, 1, 1, 1, 1, 1, 5, 18, 18, 33, 33, 33, 33, 33, 47, 48, 201, 201, 201, 201, 201, 201, 201, 201, 33, 1, 1, 1, 2, 2, 2, 1, 1, 5, 18, 33, 33, 33, 48, 48, 201, 201, 201, 201, 33, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 280
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037077 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037077
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037077/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037077
Building REAL300000037078
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037078'
/scratch/stefan/7769618/working/building/REAL300000037078 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037078

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037078/0 /scratch/stefan/7769618/working/building/REAL300000037078 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/83
`/scratch/stefan/7769618/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1Cl)

`REAL300000037078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037078 none CC1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [63, 35, 64, 64, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 22, 40, 40, 1, 64, 64, 64, 64, 64, 64, 64, 64, 22, 6, 1, 1, 1, 22, 22, 1, 64] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35])
total number of confs: 353
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: REAL300000037078 none CC1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 30, 30, 64, 64, 64, 64, 64, 140, 201, 201, 201, 64, 1, 1, 1, 2, 2, 2, 1, 1, 9, 30, 64, 64, 64, 201, 201, 64, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 543
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037078 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037078
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037078/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037078
Building REAL300000037079
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037079'
/scratch/stefan/7769618/working/building/REAL300000037079 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037079

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037079/0 /scratch/stefan/7769618/working/building/REAL300000037079 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/84
`/scratch/stefan/7769618/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C=C1Cl)

`REAL300000037079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037079 none CC1=CC=C(NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [51, 29, 51, 51, 16, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 23, 23, 28, 28, 23, 23, 23, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 16, 4, 1, 1, 10, 10, 23, 23, 1, 1, 51] 144
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, 42])
total number of confs: 238
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037079 none CC1=CC=C(NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 134, 144, 144, 82, 49, 49, 23, 23, 23, 23, 14, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 23, 23, 144, 144, 144, 144, 144, 144, 144, 144, 82, 49, 22, 23, 6, 6, 1, 1, 23, 23, 144] 144
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, 42])
total number of confs: 387
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037079 none CC1=CC=C(NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 34, 34, 51, 51, 34, 34, 69, 88, 144, 144, 144, 144, 144, 144, 144, 51, 51, 1, 1, 1, 2, 2, 2, 1, 1, 10, 34, 51, 51, 88, 88, 144, 144, 51, 51, 1] 144
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 370
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037079 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037079
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037079/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037079
Building REAL300000037080
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037080'
/scratch/stefan/7769618/working/building/REAL300000037080 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037080

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037080/0 /scratch/stefan/7769618/working/building/REAL300000037080 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/85
`/scratch/stefan/7769618/working/3D/85' -> `0.mol2'
Preparing input files

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

`REAL300000037080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037080 none COC1=CC=C(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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: [68, 46, 23, 46, 46, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 119, 196, 201, 201, 46, 68, 68, 68, 46, 46, 23, 7, 1, 1, 2, 2, 2, 1, 196, 196, 46] 201
rigid atoms, others: [32, 36, 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, 33, 34, 35, 37, 38, 39])
total number of confs: 728
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037080 none COC1=CC=C(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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: [2, 1, 1, 1, 1, 1, 1, 4, 4, 13, 46, 46, 46, 46, 46, 46, 46, 1, 1, 8, 39, 76, 76, 1, 3, 3, 3, 1, 1, 4, 13, 46, 46, 46, 46, 46, 46, 39, 39, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 17, 18, 23, 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, 36, 37, 38])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037080 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037080
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037080/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037080
Building REAL300000037081
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037081'
/scratch/stefan/7769618/working/building/REAL300000037081 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037081

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037081/0 /scratch/stefan/7769618/working/building/REAL300000037081 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/86
`/scratch/stefan/7769618/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1Cl)

`REAL300000037081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037081 none CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 16, 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, 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: [29, 28, 29, 29, 7, 3, 3, 1, 1, 1, 1, 1, 1, 12, 49, 49, 49, 76, 76, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 7, 3, 1, 1, 1, 1, 29] 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, 35])
total number of confs: 308
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037081 none CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 16, 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, 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, 7, 18, 18, 29, 29, 18, 18, 101, 200, 201, 201, 201, 201, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 7, 18, 29, 29, 29, 29, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 634
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037081 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037081
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037081/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037081
Building REAL300000037082
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037082'
/scratch/stefan/7769618/working/building/REAL300000037082 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037082

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037082/0 /scratch/stefan/7769618/working/building/REAL300000037082 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/87
`/scratch/stefan/7769618/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1Cl)

`REAL300000037082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037082 none CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 29, 11, 1, 2, 2, 2, 55] 55
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31])
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: REAL300000037082 none CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 40, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 2, 2, 2, 1, 1, 10, 40, 55, 55, 55, 55, 1] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037082 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037082
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037082/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037082
Building REAL300000037083
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037083'
/scratch/stefan/7769618/working/building/REAL300000037083 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037083

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037083/0 /scratch/stefan/7769618/working/building/REAL300000037083 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/88
`/scratch/stefan/7769618/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1Cl)

`REAL300000037083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037083 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 16, 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, 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: [70, 70, 70, 70, 22, 7, 7, 1, 1, 1, 1, 1, 1, 7, 33, 60, 60, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 22, 7, 1, 1, 33, 33, 1, 70] 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, 35])
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: REAL300000037083 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 16, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 25, 25, 70, 70, 39, 68, 154, 201, 201, 201, 70, 70, 70, 1, 1, 1, 2, 2, 2, 1, 1, 6, 25, 70, 70, 201, 201, 70, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 598
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037083 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037083
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037083/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037083
Building REAL300000037084
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037084'
/scratch/stefan/7769618/working/building/REAL300000037084 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037084

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037084/0 /scratch/stefan/7769618/working/building/REAL300000037084 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/89
`/scratch/stefan/7769618/working/3D/89' -> `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=C(C)C(Cl)=C2)C=C1)

`REAL300000037084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037084 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 56, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 55, 12, 1, 1, 2, 2, 2, 1, 81, 81] 81
rigid atoms, others: [32, 36, 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, 33, 34, 35, 37, 38])
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: REAL300000037084 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 29, 81, 81, 72, 81, 81, 81, 81, 1, 1, 4, 4, 4, 1, 10, 29, 81, 81, 81, 81, 81, 81, 1, 1] 81
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 23, 24, 38, 28, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037084 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037084
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037084/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037084
Building REAL300000037085
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037085'
/scratch/stefan/7769618/working/building/REAL300000037085 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037085

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037085/0 /scratch/stefan/7769618/working/building/REAL300000037085 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/90
`/scratch/stefan/7769618/working/3D/90' -> `0.mol2'
Preparing input files

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

`REAL300000037085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037085 none CCC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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]
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: [20, 7, 1, 7, 7, 38, 91, 91, 85, 91, 91, 91, 91, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 38, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1] 100
rigid atoms, others: [34, 35, 36, 37, 13, 2, 14, 15, 16, 17, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 263
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: REAL300000037085 none CCC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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]
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: [85, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 91, 91, 59, 68, 91, 91, 91, 91, 85, 85, 85, 85, 85, 11, 1, 1, 2, 2, 2, 1, 91, 91, 91, 91] 100
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 478
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037085 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037085
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037085/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037085
Building REAL300000037086
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037086'
/scratch/stefan/7769618/working/building/REAL300000037086 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037086

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037086/0 /scratch/stefan/7769618/working/building/REAL300000037086 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/91
`/scratch/stefan/7769618/working/3D/91' -> `0.mol2'
Preparing input files

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

`REAL300000037086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037086 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC=C1C(=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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 2, 2, 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, 7, 26, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 26, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1] 60
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037086 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC=C1C(=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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 60, 60, 59, 60, 60, 60, 60, 60, 41, 41, 41, 11, 1, 1, 2, 2, 2, 1, 60, 60, 60, 60] 60
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037086 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037086
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037086/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037086
Building REAL300000037087
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037087'
/scratch/stefan/7769618/working/building/REAL300000037087 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037087

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037087/0 /scratch/stefan/7769618/working/building/REAL300000037087 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/92
`/scratch/stefan/7769618/working/3D/92' -> `0.mol2'
Preparing input files

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

`REAL300000037087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037087 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 42, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 42, 90, 90, 90, 90, 90, 90, 1, 1, 1, 2] 180
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 180
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: REAL300000037087 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 90, 90, 90, 90, 90, 90, 90, 90, 90, 43, 43, 43, 12, 1, 1, 2, 2, 2, 1, 90, 90, 90, 180] 180
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 331
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037087 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037087
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037087/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037087
Building REAL300000037088
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037088'
/scratch/stefan/7769618/working/building/REAL300000037088 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037088

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037088/0 /scratch/stefan/7769618/working/building/REAL300000037088 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/93
`/scratch/stefan/7769618/working/3D/93' -> `0.mol2'
Preparing input files

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

`REAL300000037088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037088 none CCC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [31, 12, 1, 12, 12, 63, 174, 174, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 63, 174, 174, 174, 174, 174, 174, 1, 1, 1] 201
rigid atoms, others: [2, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 394
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: REAL300000037088 none CCC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [103, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 174, 174, 174, 174, 174, 174, 174, 174, 174, 103, 103, 103, 103, 103, 10, 1, 1, 2, 2, 2, 1, 174, 174, 174] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37])
total number of confs: 525
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037088 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037088
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037088/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037088
Building REAL300000037089
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037089'
/scratch/stefan/7769618/working/building/REAL300000037089 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037089

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037089/0 /scratch/stefan/7769618/working/building/REAL300000037089 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/94
`/scratch/stefan/7769618/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1Cl)

`REAL300000037089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037089 none CC1=CC=C(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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]
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, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 25, 6, 1, 1, 1, 1, 42] 42
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037089 none CC1=CC=C(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 35, 35, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 2, 2, 2, 1, 1, 13, 35, 42, 42, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037089 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037089/1 /scratch/stefan/7769618/working/building/REAL300000037089 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/95
`/scratch/stefan/7769618/working/3D/95' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1Cl)

`REAL300000037089.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037089/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037089 none CC1=CC=C(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [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]
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: [64, 64, 64, 64, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 64, 64, 64, 65, 65, 65, 64, 64, 34, 8, 1, 1, 1, 1, 64] 65
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 15, 16, 20, 21, 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: REAL300000037089 none CC1=CC=C(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 44, 44, 64, 64, 64, 64, 64, 64, 65, 65, 64, 64, 64, 1, 1, 1, 2, 2, 2, 1, 1, 10, 44, 64, 64, 64, 64, 1] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037089 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037089
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037089/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037089/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037089
Building REAL300000037090
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037090'
/scratch/stefan/7769618/working/building/REAL300000037090 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037090

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037090/0 /scratch/stefan/7769618/working/building/REAL300000037090 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/96
`/scratch/stefan/7769618/working/3D/96' -> `0.mol2'
Preparing input files

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

`REAL300000037090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037090 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 42, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 42, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1] 82
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 175
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: REAL300000037090 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 82, 82, 82, 82, 82, 82, 82, 82, 44, 44, 44, 12, 1, 1, 2, 2, 2, 1, 82, 82, 82, 82] 82
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 143
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037090 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037090
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037090/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037090
Building REAL300000037091
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037091'
/scratch/stefan/7769618/working/building/REAL300000037091 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037091

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037091/0 /scratch/stefan/7769618/working/building/REAL300000037091 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/97
`/scratch/stefan/7769618/working/3D/97' -> `0.mol2'
Preparing input files

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

`REAL300000037091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037091 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 49, 148, 148, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 49, 148, 148, 148, 148, 148, 148, 1, 1, 1] 148
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 260
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037091 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 148, 148, 148, 148, 148, 148, 148, 148, 148, 58, 58, 58, 12, 1, 1, 2, 2, 2, 1, 148, 148, 148] 148
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34])
total number of confs: 227
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037091 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037091
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037091/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037091
Building REAL300000037092
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037092'
/scratch/stefan/7769618/working/building/REAL300000037092 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037092

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037092/0 /scratch/stefan/7769618/working/building/REAL300000037092 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/98
`/scratch/stefan/7769618/working/3D/98' -> `0.mol2'
Preparing input files

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

`REAL300000037092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037092 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 69, 69, 69, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 179, 201, 201, 201, 122, 122, 122, 69, 26, 7, 1, 1, 2, 2, 2, 1, 69, 201, 201] 201
rigid atoms, others: [33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41])
total number of confs: 490
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: REAL300000037092 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 69, 69, 64, 69, 69, 69, 69, 1, 1, 2, 2, 1, 1, 1, 9, 17, 23, 23, 4, 4, 4, 1, 7, 21, 69, 69, 69, 69, 69, 69, 1, 17, 17] 201
rigid atoms, others: [1, 2, 3, 4, 5, 39, 16, 17, 20, 21, 22, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 230
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037092 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037092
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037092/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037092
Building REAL300000037093
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037093'
/scratch/stefan/7769618/working/building/REAL300000037093 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037093

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037093/0 /scratch/stefan/7769618/working/building/REAL300000037093 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/99
`/scratch/stefan/7769618/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1Cl)

`REAL300000037093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037093 none CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [41, 38, 41, 41, 12, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 15, 22, 22, 41, 41, 41, 41, 41, 41, 41, 41, 12, 4, 1, 1, 1, 4, 4, 4, 15, 15, 41] 60
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, 42])
total number of confs: 164
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037093 none CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
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, 11, 30, 30, 41, 41, 41, 41, 41, 41, 30, 41, 41, 41, 46, 46, 60, 60, 60, 1, 1, 1, 2, 2, 2, 1, 1, 11, 30, 41, 41, 41, 46, 46, 46, 60, 60, 1] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 218
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037093 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037093
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037093/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037093
Building REAL300000037094
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037094'
/scratch/stefan/7769618/working/building/REAL300000037094 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037094

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037094/0 /scratch/stefan/7769618/working/building/REAL300000037094 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/100
`/scratch/stefan/7769618/working/3D/100' -> `0.mol2'
Preparing input files

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

`REAL300000037094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037094 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 25, 76, 76, 53, 76, 76, 76, 76, 1, 1, 1, 1, 1, 9, 19, 19, 11, 11, 19, 19, 19, 19, 1, 1, 6, 6, 6, 25, 76, 76, 76, 76, 76, 76, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 45, 38, 39, 44, 12, 13, 14, 15, 16, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 291
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037094 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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: [59, 9, 59, 59, 122, 201, 201, 201, 201, 201, 201, 201, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 59, 59, 59, 122, 201, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 511
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037094 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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: [34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 76, 76, 34, 36, 185, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 35, 35, 35, 6, 1, 1, 2, 2, 2, 1, 76, 76, 201, 201, 201, 201, 76, 76] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 419
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037094 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037094
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037094/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037094
Building REAL300000037095
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037095'
/scratch/stefan/7769618/working/building/REAL300000037095 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037095

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037095/0 /scratch/stefan/7769618/working/building/REAL300000037095 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/101
`/scratch/stefan/7769618/working/3D/101' -> `0.mol2'
Preparing input files

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

`REAL300000037095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037095 none COC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 47, 47, 17, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 127, 186, 186, 201, 193, 77, 77, 77, 47, 16, 6, 1, 1, 2, 2, 2, 1, 47, 47, 186, 186, 186, 186] 201
rigid atoms, others: [32, 36, 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, 37, 38, 39, 40, 41, 42])
total number of confs: 616
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037095 none COC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 9, 25, 26, 38, 36, 3, 3, 3, 1, 7, 15, 47, 47, 47, 47, 47, 47, 1, 1, 25, 25, 25, 25] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 28, 37] 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, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037095 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037095
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037095/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037095
Building REAL300000037096
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037096'
/scratch/stefan/7769618/working/building/REAL300000037096 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037096

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037096/0 /scratch/stefan/7769618/working/building/REAL300000037096 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/102
`/scratch/stefan/7769618/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1Cl)

`REAL300000037096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037096 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 16, 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, 2, 2, 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, 21, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 21, 8, 1, 1, 1, 38] 38
rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037096 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 30, 30, 38, 38, 30, 38, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 1, 10, 30, 38, 38, 38, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037096 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037096
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037096/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037096
Building REAL300000037097
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037097'
/scratch/stefan/7769618/working/building/REAL300000037097 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037097

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037097/0 /scratch/stefan/7769618/working/building/REAL300000037097 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/103
`/scratch/stefan/7769618/working/3D/103' -> `0.mol2'
Preparing input files

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

`REAL300000037097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037097 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 50, 139, 139, 138, 139, 139, 139, 139, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 50, 139, 139, 139, 139, 139, 139, 1, 2, 2, 2, 2, 2, 2] 139
rigid atoms, others: [1, 33, 12, 13, 14, 15, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 268
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037097 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 54, 54, 54, 12, 1, 1, 2, 2, 2, 1, 139, 139, 139, 139, 139, 139, 139] 139
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 215
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037097 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037097
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037097/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037097
Building REAL300000037098
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037098'
/scratch/stefan/7769618/working/building/REAL300000037098 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037098

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037098/0 /scratch/stefan/7769618/working/building/REAL300000037098 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/104
`/scratch/stefan/7769618/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1Cl)

`REAL300000037098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037098 none CC1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
1  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 31, 31, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 31, 31, 31, 18, 6, 1, 1, 2, 1, 31] 62
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
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: REAL300000037098 none CC1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
1  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 24, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 1, 1, 11, 24, 31, 31, 62, 31, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037098 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037098
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037098/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037098
Building REAL300000037099
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037099'
/scratch/stefan/7769618/working/building/REAL300000037099 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037099

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037099/0 /scratch/stefan/7769618/working/building/REAL300000037099 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/105
`/scratch/stefan/7769618/working/3D/105' -> `0.mol2'
Preparing input files

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

`REAL300000037099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037099 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 35, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 35, 72, 72, 72, 72, 72, 72, 1, 1, 1, 2, 2, 2] 72
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37])
total number of confs: 159
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037099 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 72, 72, 72, 72, 72, 72, 72, 72, 72, 41, 41, 41, 12, 1, 1, 2, 2, 2, 1, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 130
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037099 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037099
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037099/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037099
Building REAL300000037100
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037100'
/scratch/stefan/7769618/working/building/REAL300000037100 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037100

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037100/0 /scratch/stefan/7769618/working/building/REAL300000037100 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/106
`/scratch/stefan/7769618/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl)

`REAL300000037100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037100 none CC1=CC=C(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 66, 66, 17, 4, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 43, 43, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 17, 4, 1, 1, 31, 31, 31, 31, 1, 1, 66] 201
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38])
total number of confs: 366
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: REAL300000037100 none CC1=CC=C(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 38, 38, 66, 66, 38, 38, 151, 198, 198, 201, 201, 66, 66, 1, 1, 1, 2, 2, 2, 1, 1, 10, 38, 66, 66, 198, 198, 198, 198, 66, 66, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 606
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037100 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037100
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037100/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037100
Building REAL300000037101
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037101'
/scratch/stefan/7769618/working/building/REAL300000037101 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037101

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037101/0 /scratch/stefan/7769618/working/building/REAL300000037101 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/107
`/scratch/stefan/7769618/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1Cl)

`REAL300000037101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037101 none CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 83, 114, 114, 43, 9, 9, 1, 1, 1, 1, 1, 8, 16, 16, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 114, 43, 9, 1, 8, 8, 1, 1, 1, 1, 114] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 38])
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: REAL300000037101 none CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 43, 43, 114, 114, 114, 201, 201, 201, 114, 114, 114, 114, 114, 114, 1, 1, 1, 2, 2, 2, 1, 1, 10, 43, 114, 201, 201, 114, 114, 114, 114, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 598
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037101 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037101
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037101/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037101
Building REAL300000037102
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037102'
/scratch/stefan/7769618/working/building/REAL300000037102 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037102

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037102/0 /scratch/stefan/7769618/working/building/REAL300000037102 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/108
`/scratch/stefan/7769618/working/3D/108' -> `0.mol2'
Preparing input files

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

`REAL300000037102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037102 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 19, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 5, 19, 32, 44, 59, 59, 1, 9, 9, 9, 19, 31, 31, 31, 31, 31, 31, 1, 1, 1, 19, 19, 31, 31, 44, 44, 1] 201
rigid atoms, others: [1, 35, 36, 37, 44, 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, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 315
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: REAL300000037102 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 1, 6, 31, 31, 31, 31, 31, 87, 138, 165, 201, 201, 201, 31, 7, 7, 7, 2, 1, 1, 2, 2, 2, 1, 31, 31, 31, 138, 138, 165, 165, 201, 201, 31] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 731
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037102 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037102
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037102/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037102
Building REAL300000037103
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037103'
/scratch/stefan/7769618/working/building/REAL300000037103 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037103

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037103/0 /scratch/stefan/7769618/working/building/REAL300000037103 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/109
`/scratch/stefan/7769618/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl)

`REAL300000037103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037103 none CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 28, 28, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 11, 26, 26, 35, 35, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 26, 26, 26, 26, 1, 1, 60] 201
rigid atoms, others: [45, 39, 40, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 47])
total number of confs: 207
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037103 none CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 6, 31, 31, 59, 60, 60, 60, 60, 60, 177, 201, 201, 201, 201, 60, 60, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 31, 31, 60, 60, 60, 60, 60, 60, 201, 201, 201, 201, 60, 60, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 549
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037103 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037103
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037103/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037103
Building REAL300000037104
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037104'
/scratch/stefan/7769618/working/building/REAL300000037104 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037104

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037104/0 /scratch/stefan/7769618/working/building/REAL300000037104 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/110
`/scratch/stefan/7769618/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl)

`REAL300000037104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037104 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 34, 34, 8, 3, 8, 2, 1, 1, 1, 1, 1, 1, 6, 22, 37, 37, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 22, 22, 1, 1, 72] 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, 44])
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: REAL300000037104 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 6, 32, 32, 68, 72, 72, 72, 72, 72, 152, 201, 201, 201, 72, 72, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 32, 71, 71, 72, 71, 72, 72, 201, 201, 72, 72, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 675
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037104 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037104
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037104/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037104
Building REAL300000037105
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037105'
/scratch/stefan/7769618/working/building/REAL300000037105 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037105

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037105/0 /scratch/stefan/7769618/working/building/REAL300000037105 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/111
`/scratch/stefan/7769618/working/3D/111' -> `0.mol2'
Preparing input files

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

`REAL300000037105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037105 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 23, 69, 69, 40, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 11, 25, 25, 33, 33, 1, 9, 9, 9, 23, 69, 69, 69, 69, 69, 69, 1, 1, 1, 25, 25, 25, 25, 1] 201
rigid atoms, others: [1, 34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 343
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037105 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 69, 69, 69, 69, 69, 168, 201, 201, 201, 201, 69, 27, 27, 27, 6, 1, 1, 2, 2, 2, 1, 69, 69, 69, 201, 201, 201, 201, 69] 201
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 437
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037105 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037105
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037105/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037105
Building REAL300000037106
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037106'
/scratch/stefan/7769618/working/building/REAL300000037106 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037106

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037106/0 /scratch/stefan/7769618/working/building/REAL300000037106 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/112
`/scratch/stefan/7769618/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl)

`REAL300000037106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037106 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 36, 36, 9, 3, 9, 2, 1, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 14, 14, 14, 14, 1, 1, 68] 201
rigid atoms, others: [45, 39, 40, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 47])
total number of confs: 189
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: REAL300000037106 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 6, 32, 32, 64, 70, 70, 70, 70, 70, 195, 201, 201, 201, 201, 70, 70, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 32, 68, 68, 70, 69, 70, 70, 201, 201, 201, 201, 70, 70, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 510
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037106 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037106
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037106/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037106
Building REAL300000037107
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037107'
/scratch/stefan/7769618/working/building/REAL300000037107 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037107

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037107/0 /scratch/stefan/7769618/working/building/REAL300000037107 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/113
`/scratch/stefan/7769618/working/3D/113' -> `0.mol2'
Preparing input files

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

`REAL300000037107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037107 none CCC(=NNC1=CC=C(C)C(Cl)=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.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 7, 7, 18, 33, 33, 31, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 7, 19, 19, 32, 38, 39, 1, 1, 10, 10, 10, 10, 10, 18, 33, 33, 33, 33, 33, 33, 1, 1, 7, 7, 19, 19, 19, 20, 31, 31, 1, 1] 201
rigid atoms, others: [2, 49, 39, 40, 13, 14, 15, 16, 17, 50, 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, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 257
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: REAL300000037107 none CCC(=NNC1=CC=C(C)C(Cl)=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.3', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 12, 14, 77, 102, 150, 150, 184, 194, 195, 33, 33, 18, 18, 18, 18, 18, 4, 1, 1, 2, 2, 2, 1, 33, 33, 100, 100, 150, 150, 150, 150, 184, 184, 33, 33] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 798
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037107 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037107
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037107/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037107
Building REAL300000037108
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037108'
/scratch/stefan/7769618/working/building/REAL300000037108 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037108

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037108/0 /scratch/stefan/7769618/working/building/REAL300000037108 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/114
`/scratch/stefan/7769618/working/3D/114' -> `0.mol2'
Preparing input files

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

`REAL300000037108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037108 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 1, 12, 12, 47, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 47, 92, 92, 92, 92, 92, 92, 1, 1] 92
rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037108 none CC(=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 92, 92, 92, 92, 92, 92, 92, 34, 34, 34, 10, 1, 1, 2, 2, 2, 1, 92, 92] 92
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31])
total number of confs: 147
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037108 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037108
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037108/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037108
Building REAL300000037109
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037109'
/scratch/stefan/7769618/working/building/REAL300000037109 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037109

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037109/0 /scratch/stefan/7769618/working/building/REAL300000037109 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/115
`/scratch/stefan/7769618/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1Cl)

`REAL300000037109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037109 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 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, 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: [32, 27, 32, 32, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 1, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1, 32] 46
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 13, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 38])
total number of confs: 81
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037109 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 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, 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, 44, 46, 46, 26, 26, 5, 5, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 46] 46
rigid atoms, others: [32, 33, 34, 35, 9, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 94
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037109 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 46, 46, 32, 46, 46, 44, 46, 46, 32, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 46, 46, 44, 46, 46, 32, 32, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 160
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037109 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037109
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037109/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037109
Building REAL300000037110
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037110'
/scratch/stefan/7769618/working/building/REAL300000037110 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037110

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037110/0 /scratch/stefan/7769618/working/building/REAL300000037110 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/116
`/scratch/stefan/7769618/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1Cl)

`REAL300000037110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037110 none CC1=CC=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [51, 37, 51, 51, 19, 19, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 4, 4, 4, 4, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2, 51] 75
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300000037110 none CC1=CC=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 51, 51, 51, 51, 51, 75, 75, 75, 51, 51, 51, 1, 1, 1, 2, 2, 2, 1, 1, 34, 34, 34, 34, 51, 51, 75, 75, 51, 51, 51, 51, 51, 51, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037110 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037110
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037110/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037110
Building REAL300000037111
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037111'
/scratch/stefan/7769618/working/building/REAL300000037111 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037111

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037111/0 /scratch/stefan/7769618/working/building/REAL300000037111 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/117
`/scratch/stefan/7769618/working/3D/117' -> `0.mol2'
Preparing input files

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

`REAL300000037111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037111 none CC1=CC=C(N=NC(C)CCCCCCC(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 69, 79, 90, 117, 126, 200, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 32, 72, 72, 76, 79, 95, 95, 112, 117, 133, 133, 195, 200, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 995
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037111 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037111
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037111/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037111
Building REAL300000037112
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037112'
/scratch/stefan/7769618/working/building/REAL300000037112 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037112

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037112/0 /scratch/stefan/7769618/working/building/REAL300000037112 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/118
`/scratch/stefan/7769618/working/3D/118' -> `0.mol2'
Preparing input files

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

`REAL300000037112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037112 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 51, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 51, 95, 95, 95, 95, 95, 95, 1, 1] 95
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 195
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037112 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 95, 95, 95, 95, 95, 95, 95, 55, 55, 55, 10, 1, 1, 2, 2, 2, 1, 95, 95] 95
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037112 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037112
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037112/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037112
Building REAL300000037113
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037113'
/scratch/stefan/7769618/working/building/REAL300000037113 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037113

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037113/0 /scratch/stefan/7769618/working/building/REAL300000037113 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/119
`/scratch/stefan/7769618/working/3D/119' -> `0.mol2'
Preparing input files

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

`REAL300000037113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037113 none COC1=CC(C(C)=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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, 7, 7, 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: [72, 46, 46, 46, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 106, 178, 186, 201, 201, 201, 72, 72, 72, 46, 14, 14, 14, 4, 1, 1, 2, 2, 2, 1, 46, 46, 178, 178, 186, 186, 201, 201] 201
rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 679
number of broken/clashed sets: 126
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037113 none COC1=CC(C(C)=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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, 7, 7, 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, 7, 7, 7, 21, 46, 46, 45, 46, 46, 46, 46, 1, 1, 1, 1, 7, 15, 18, 26, 37, 37, 3, 3, 3, 1, 7, 7, 7, 21, 46, 46, 46, 46, 46, 46, 1, 1, 15, 15, 17, 17, 26, 26] 201
rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 17, 18, 19, 20, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 257
number of broken/clashed sets: 126
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037113 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037113
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037113/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037113
Building REAL300000037114
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037114'
/scratch/stefan/7769618/working/building/REAL300000037114 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037114

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037114/0 /scratch/stefan/7769618/working/building/REAL300000037114 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/120
`/scratch/stefan/7769618/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C=C1Cl)

`REAL300000037114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037114 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'Cl', 'C.ar', 'C.3', 'C.ar', '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, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 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: [23, 17, 22, 22, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 9, 9, 9, 9, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 1, 1, 23] 54
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 13, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 38])
total number of confs: 79
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037114 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'Cl', 'C.ar', 'C.3', 'C.ar', '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, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 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, 48, 54, 54, 28, 28, 9, 9, 9, 1, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 9, 54, 54, 54, 54, 54, 54, 54, 54, 9, 9, 9, 1, 1, 1, 1, 9, 9, 54] 54
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, 38])
total number of confs: 135
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037114 none CC1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'Cl', 'C.ar', 'C.3', 'C.ar', '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, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 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, 9, 9, 23, 23, 23, 26, 26, 23, 54, 54, 54, 54, 54, 54, 23, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 23, 54, 54, 54, 54, 23, 23, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 115
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037114 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037114
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037114/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037114
Building REAL300000037115
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037115'
/scratch/stefan/7769618/working/building/REAL300000037115 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037115

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037115/0 /scratch/stefan/7769618/working/building/REAL300000037115 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/121
`/scratch/stefan/7769618/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl)

`REAL300000037115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037115 none CC1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 38, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 30
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: REAL300000037115 none CC1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 39
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037115 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037115
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037115/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037115
Building REAL300000037116
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037116'
/scratch/stefan/7769618/working/building/REAL300000037116 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000037116 as failed and skipping
/scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `/scratch/stefan/7769618/failed'
`/scratch/stefan/7769618/working/building/REAL300000037116' -> `/scratch/stefan/7769618/failed/REAL300000037116'
Building REAL300000037117
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037117'
/scratch/stefan/7769618/working/building/REAL300000037117 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037117

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037117/0 /scratch/stefan/7769618/working/building/REAL300000037117 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/122
`/scratch/stefan/7769618/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1Cl)

`REAL300000037117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037117 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
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, 53, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 53, 13, 1, 2, 2, 2, 1, 2, 2, 2, 130] 130
rigid atoms, others: [33, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37])
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: REAL300000037117 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
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, 1, 1, 10, 50, 50, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 2, 2, 2, 1, 1, 10, 50, 130, 130, 130, 130, 130, 130, 130, 130, 1] 130
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037117 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037117
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037117/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037117
Building REAL300000037118
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037118'
/scratch/stefan/7769618/working/building/REAL300000037118 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037118

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037118/0 /scratch/stefan/7769618/working/building/REAL300000037118 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/123
`/scratch/stefan/7769618/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1Cl)

`REAL300000037118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037118 none CC1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 16, 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, 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, 36, 38, 38, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 19, 6, 1, 1, 1, 38] 38
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037118 none CC1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 16, 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, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 31, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 1, 10, 31, 38, 38, 38, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037118 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037118
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037118/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037118
Building REAL300000037119
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037119'
/scratch/stefan/7769618/working/building/REAL300000037119 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037119

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037119/0 /scratch/stefan/7769618/working/building/REAL300000037119 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/124
`/scratch/stefan/7769618/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl)

`REAL300000037119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037119 none CC1=CC=C(NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 22
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 41, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037119 none CC1=CC=C(NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 1, 1, 1, 2, 2, 2, 1, 1, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037119 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037119
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037119/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037119
Building REAL300000037120
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037120'
/scratch/stefan/7769618/working/building/REAL300000037120 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037120

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037120/0 /scratch/stefan/7769618/working/building/REAL300000037120 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/125
`/scratch/stefan/7769618/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1Cl)

`REAL300000037120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037120 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [42, 40, 43, 43, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 26, 34, 34, 26, 33, 33, 26, 33, 33, 1, 43, 43, 43, 43, 43, 43, 43, 43, 13, 5, 1, 1, 1, 26, 33, 33, 26, 33, 33, 1, 43] 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, 45])
total number of confs: 232
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037120 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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, 201, 201, 137, 77, 77, 33, 33, 33, 33, 33, 8, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 33, 201, 201, 201, 201, 201, 201, 201, 201, 137, 77, 33, 33, 33, 3, 1, 1, 1, 1, 1, 33, 201] 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, 45])
total number of confs: 511
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037120 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 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, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 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: [1, 1, 1, 1, 1, 1, 8, 23, 23, 43, 43, 43, 43, 43, 122, 197, 201, 201, 197, 201, 201, 197, 201, 201, 43, 1, 1, 1, 2, 2, 2, 1, 1, 8, 23, 43, 43, 43, 197, 201, 201, 197, 201, 201, 43, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 586
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037120 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037120
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037120/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037120
Building REAL300000037121
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037121'
/scratch/stefan/7769618/working/building/REAL300000037121 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037121

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037121/0 /scratch/stefan/7769618/working/building/REAL300000037121 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/126
`/scratch/stefan/7769618/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1Cl)

`REAL300000037121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037121 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [82, 81, 83, 83, 23, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 23, 8, 1, 1, 1, 83] 83
rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
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: REAL300000037121 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 46, 46, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 2, 2, 2, 1, 1, 13, 46, 83, 83, 83, 1] 83
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037121 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037121
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037121/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037121
Building REAL300000037122
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037122'
/scratch/stefan/7769618/working/building/REAL300000037122 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037122

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037122/0 /scratch/stefan/7769618/working/building/REAL300000037122 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/127
`/scratch/stefan/7769618/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1Cl)

`REAL300000037122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037122 none CC1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 16, 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, 2, 2, 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: [87, 57, 87, 87, 25, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 1, 87, 87, 87, 87, 87, 87, 87, 87, 25, 7, 1, 1, 12, 12, 87] 141
rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32])
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: REAL300000037122 none CC1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 16, 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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 11, 49, 49, 87, 87, 87, 87, 140, 140, 141, 141, 87, 1, 1, 1, 2, 2, 2, 1, 1, 11, 49, 87, 87, 140, 140, 1] 141
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037122 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037122
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037122/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037122
Building REAL300000037123
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037123'
/scratch/stefan/7769618/working/building/REAL300000037123 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037123

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037123/0 /scratch/stefan/7769618/working/building/REAL300000037123 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/128
`/scratch/stefan/7769618/working/3D/128' -> `0.mol2'
Preparing input files

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

`REAL300000037123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037123 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 35, 157, 157, 125, 157, 157, 157, 157, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 17, 17, 7, 7, 7, 35, 157, 157, 157, 157, 157, 157, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 201
rigid atoms, others: [1, 35, 36, 37, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 445
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: REAL300000037123 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 157, 157, 157, 157, 157, 157, 157, 157, 157, 201, 201, 201, 54, 54, 54, 10, 1, 1, 2, 2, 2, 1, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 318
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037123 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037123
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037123/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037123
Building REAL300000037124
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037124'
/scratch/stefan/7769618/working/building/REAL300000037124 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037124

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037124/0 /scratch/stefan/7769618/working/building/REAL300000037124 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/129
`/scratch/stefan/7769618/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1Cl)

`REAL300000037124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037124 none CC1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 14, 14, 14, 15, 15, 15, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14] 15
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037124 none CC1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
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, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 14, 1, 1, 1, 2, 2, 2, 1, 1, 10, 14, 14, 14, 14, 14, 14, 14, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037124 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037124
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037124/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037124
Building REAL300000037125
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037125'
/scratch/stefan/7769618/working/building/REAL300000037125 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037125

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037125/0 /scratch/stefan/7769618/working/building/REAL300000037125 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/130
`/scratch/stefan/7769618/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl)

`REAL300000037125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037125 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [33, 28, 33, 33, 15, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 3, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 15, 5, 1, 1, 3, 3, 3, 3, 1, 1, 33] 43
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, 41])
total number of confs: 89
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037125 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 23, 9, 8, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 23, 8, 3, 3, 1, 1, 1, 1, 3, 3, 43] 43
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 96
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037125 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 31, 31, 33, 33, 31, 31, 43, 43, 33, 43, 43, 43, 43, 43, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 11, 31, 33, 33, 43, 43, 43, 43, 33, 33, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 141
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037125 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037125
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037125/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037125
Building REAL300000037126
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037126'
/scratch/stefan/7769618/working/building/REAL300000037126 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037126

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037126/0 /scratch/stefan/7769618/working/building/REAL300000037126 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/131
`/scratch/stefan/7769618/working/3D/131' -> `0.mol2'
Preparing input files

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

`REAL300000037126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037126 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 50, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 50, 90, 90, 90, 90, 90, 90, 1, 1, 1] 90
rigid atoms, others: [32, 1, 33, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 190
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037126 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [43, 44, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 90, 90, 90, 90, 90, 90, 90, 90, 44, 44, 44, 13, 1, 1, 2, 2, 2, 1, 90, 90, 90] 90
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33])
total number of confs: 148
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037126 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037126
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037126/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037126
Building REAL300000037127
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037127'
/scratch/stefan/7769618/working/building/REAL300000037127 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037127

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037127/0 /scratch/stefan/7769618/working/building/REAL300000037127 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/132
`/scratch/stefan/7769618/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1Cl)

`REAL300000037127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037127 none CC1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 23, 5, 1, 1, 1, 1, 1, 45] 45
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037127 none CC1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 2, 2, 2, 1, 1, 8, 35, 45, 45, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037127 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037127
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037127/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037127
Building REAL300000037128
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037128'
/scratch/stefan/7769618/working/building/REAL300000037128 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037128

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037128/0 /scratch/stefan/7769618/working/building/REAL300000037128 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/133
`/scratch/stefan/7769618/working/3D/133' -> `0.mol2'
Preparing input files

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

`REAL300000037128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037128 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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: [141, 72, 72, 72, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 71, 71, 158, 191, 191, 201, 201, 141, 141, 141, 72, 26, 6, 1, 1, 2, 2, 2, 1, 72, 191, 191, 191, 191] 201
rigid atoms, others: [32, 33, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42])
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: REAL300000037128 none COC1=CC(C=NNC2=CC=C(C)C(Cl)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 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, 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, 8, 8, 24, 72, 72, 39, 72, 72, 72, 72, 1, 1, 1, 1, 1, 5, 14, 14, 21, 21, 4, 4, 4, 1, 8, 24, 72, 72, 72, 72, 72, 72, 1, 14, 14, 14, 14] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 20, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037128 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037128
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037128/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037128
Building REAL300000037129
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037129'
/scratch/stefan/7769618/working/building/REAL300000037129 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037129

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037129/0 /scratch/stefan/7769618/working/building/REAL300000037129 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/134
`/scratch/stefan/7769618/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1Cl)

`REAL300000037129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037129 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [75, 43, 75, 75, 24, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 24, 9, 1, 1, 2, 1, 75] 150
rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037129 none CC1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 37, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 2, 2, 2, 1, 1, 11, 37, 75, 75, 150, 75, 1] 150
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037129 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037129
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037129/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037129
Building REAL300000037130
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037130'
/scratch/stefan/7769618/working/building/REAL300000037130 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037130

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037130/0 /scratch/stefan/7769618/working/building/REAL300000037130 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/135
`/scratch/stefan/7769618/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C=C1Cl)

`REAL300000037130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037130 none CC1=CC=C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 33, 33, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 33, 22, 8, 1, 1, 2, 2, 2, 1, 33] 33
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34])
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: REAL300000037130 none CC1=CC=C(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 11, 27, 33, 33, 33, 33, 33, 33, 1] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037130 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037130
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037130/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037130
Building REAL300000037131
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037131'
/scratch/stefan/7769618/working/building/REAL300000037131 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037131

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037131/0 /scratch/stefan/7769618/working/building/REAL300000037131 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/136
`/scratch/stefan/7769618/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1Cl)

`REAL300000037131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037131 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 16, 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, 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, 39, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 39, 7, 1, 93] 93
rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28])
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: REAL300000037131 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 46, 46, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 2, 2, 2, 1, 1, 12, 46, 93, 1] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037131 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037131
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037131/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037131
Building REAL300000037132
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037132'
/scratch/stefan/7769618/working/building/REAL300000037132 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037132

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037132/0 /scratch/stefan/7769618/working/building/REAL300000037132 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/137
`/scratch/stefan/7769618/working/3D/137' -> `0.mol2'
Preparing input files

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

`REAL300000037132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037132 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 33, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 33, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2] 69
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037132 none CC(=NNC1=CC=C(C)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 69, 69, 69, 69, 69, 69, 69, 69, 69, 44, 44, 44, 10, 1, 1, 2, 2, 2, 1, 69, 69, 69, 69, 69, 69] 69
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037132 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037132
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037132/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037132
Building REAL300000037133
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037133'
/scratch/stefan/7769618/working/building/REAL300000037133 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037133

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037133/0 /scratch/stefan/7769618/working/building/REAL300000037133 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/138
`/scratch/stefan/7769618/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1Cl)

`REAL300000037133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037133 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 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, 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: [109, 79, 109, 109, 38, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 109, 109, 109, 109, 109, 109, 109, 109, 38, 7, 1, 1, 12, 12, 24, 12, 109] 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, 39])
total number of confs: 349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037133 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 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, 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, 134, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 201, 134, 51, 12, 12, 1, 1, 2, 1, 201] 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, 39])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037133 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 53, 53, 109, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 1, 1, 1, 2, 2, 2, 1, 1, 11, 53, 109, 109, 201, 201, 402, 201, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 713
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037133 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037133
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037133/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037133
Building REAL300000037134
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037134'
/scratch/stefan/7769618/working/building/REAL300000037134 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037134

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037134/0 /scratch/stefan/7769618/working/building/REAL300000037134 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/139
`/scratch/stefan/7769618/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1Cl)

`REAL300000037134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037134 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 8, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 19] 19
rigid atoms, others: [32, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 39, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037134 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 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, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037134 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037134
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037134/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037134
Building REAL300000037135
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037135'
/scratch/stefan/7769618/working/building/REAL300000037135 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037135

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037135/0 /scratch/stefan/7769618/working/building/REAL300000037135 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/140
`/scratch/stefan/7769618/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1Cl)

`REAL300000037135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037135 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 44, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 6, 7, 7, 1, 90, 90, 90, 90, 90, 90, 90, 90, 44, 9, 1, 1, 7, 7, 7, 7, 90] 117
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, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037135 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [117, 117, 117, 117, 78, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 117, 117, 117, 117, 117, 117, 117, 117, 78, 37, 7, 7, 1, 1, 1, 1, 117] 117
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 282
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037135 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 51, 51, 90, 90, 90, 90, 117, 117, 90, 90, 117, 117, 117, 117, 90, 1, 1, 1, 2, 2, 2, 1, 1, 10, 51, 90, 90, 117, 117, 117, 117, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 363
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037135 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037135
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037135/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037135
Building REAL300000037136
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037136'
/scratch/stefan/7769618/working/building/REAL300000037136 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037136

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037136/0 /scratch/stefan/7769618/working/building/REAL300000037136 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/141
`/scratch/stefan/7769618/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1Cl)

`REAL300000037136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037136 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 78, 117, 117, 40, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 117, 117, 117, 117, 117, 117, 117, 117, 39, 8, 1, 1, 12, 12, 12, 12, 117] 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, 38])
total number of confs: 360
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037136 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 57, 57, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 201, 121, 57, 12, 12, 1, 1, 1, 1, 201] 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, 38])
total number of confs: 453
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037136 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 51, 51, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117, 1, 1, 1, 2, 2, 2, 1, 1, 11, 51, 117, 117, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037136 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037136
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037136/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037136
Building REAL300000037137
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037137'
/scratch/stefan/7769618/working/building/REAL300000037137 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037137

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037137/0 /scratch/stefan/7769618/working/building/REAL300000037137 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/142
`/scratch/stefan/7769618/working/3D/142' -> `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=C(C)C(Cl)=C1)

`REAL300000037137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037137 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [130, 128, 128, 128, 128, 128, 128, 128, 128, 128, 53, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 128, 128, 127, 52, 10, 1, 1, 2, 2, 2, 1] 130
rigid atoms, others: [35, 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, 34])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037137 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 127, 127, 107, 127, 127, 127, 127, 4, 4, 4, 1, 1, 1, 10, 56, 128, 127, 128, 128, 128, 127] 130
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 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: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037137 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037137
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037137/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037137
Building REAL300000037138
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037138'
/scratch/stefan/7769618/working/building/REAL300000037138 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037138

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037138/0 /scratch/stefan/7769618/working/building/REAL300000037138 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/143
`/scratch/stefan/7769618/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1Cl)

`REAL300000037138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037138 none CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 26, 6, 1, 1, 1, 1, 47] 47
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037138 none CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 35, 35, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 2, 2, 2, 1, 1, 11, 35, 47, 47, 47, 47, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037138 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037138
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037138/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037138
Building REAL300000037139
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037139'
/scratch/stefan/7769618/working/building/REAL300000037139 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037139

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037139/0 /scratch/stefan/7769618/working/building/REAL300000037139 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/144
`/scratch/stefan/7769618/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1Cl)

`REAL300000037139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037139 none CC1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 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
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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22] 22
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 37, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 34
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: REAL300000037139 none CC1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 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
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, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 1, 8, 22, 22, 22, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 43
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037139 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037139
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037139/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037139
Building REAL300000037140
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037140'
/scratch/stefan/7769618/working/building/REAL300000037140 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037140

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037140/0 /scratch/stefan/7769618/working/building/REAL300000037140 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/145
`/scratch/stefan/7769618/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1Cl)

`REAL300000037140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037140 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 16, 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, 2, 2, 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, 34, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 34, 12, 1, 1, 1, 69] 69
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, 31])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037140 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 32, 32, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 1, 1, 10, 32, 69, 69, 69, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037140 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037140
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037140/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037140
Building REAL300000037141
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037141'
/scratch/stefan/7769618/working/building/REAL300000037141 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037141

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037141/0 /scratch/stefan/7769618/working/building/REAL300000037141 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/146
`/scratch/stefan/7769618/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=C(C)C(Cl)=C2)=CC=C1C(=O)[O-])

`REAL300000037141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037141 none COC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [193, 167, 167, 167, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 193, 193, 193, 193, 193, 167, 64, 12, 1, 1, 2, 2, 2, 1, 167, 167] 193
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35])
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: REAL300000037141 none COC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 9, 9, 40, 168, 168, 76, 168, 168, 168, 167, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 9, 40, 168, 168, 168, 168, 168, 167, 1, 1] 193
rigid atoms, others: [19, 1, 2, 3, 4, 5, 34, 16, 17, 18, 35, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 564
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037141 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037141
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037141/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037141
Building REAL300000037142
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037142'
/scratch/stefan/7769618/working/building/REAL300000037142 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037142

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037142/0 /scratch/stefan/7769618/working/building/REAL300000037142 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/147
`/scratch/stefan/7769618/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1Cl)

`REAL300000037142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037142 none CC1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 35, 35, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 21, 6, 1, 1, 35] 35
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037142 none CC1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2, 1, 1, 11, 32, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037142 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037142
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037142/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037142
Building REAL300000037143
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037143'
/scratch/stefan/7769618/working/building/REAL300000037143 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037143

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037143/0 /scratch/stefan/7769618/working/building/REAL300000037143 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/148
`/scratch/stefan/7769618/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1Cl)

`REAL300000037143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037143 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
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, 7, 7, 7]
1  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 47, 26, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 25, 12, 1, 1, 2, 47] 94
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, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 103
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: REAL300000037143 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
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, 7, 7, 7]
1  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 34, 34, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 2, 2, 2, 1, 1, 11, 34, 47, 47, 94, 1] 94
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 174
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037143 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037143/1 /scratch/stefan/7769618/working/building/REAL300000037143 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/149
`/scratch/stefan/7769618/working/3D/149' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1Cl)

`REAL300000037143.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037143/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037143 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 1, 1, 17] 17
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: 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: REAL300000037143 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 8, 16, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037143 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037143
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037143/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037143/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037143
Building REAL300000037144
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037144'
/scratch/stefan/7769618/working/building/REAL300000037144 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037144

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037144/0 /scratch/stefan/7769618/working/building/REAL300000037144 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/150
`/scratch/stefan/7769618/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1Cl)

`REAL300000037144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037144 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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: [79, 78, 79, 79, 25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 12, 42, 42, 42, 42, 42, 42, 42, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 24, 5, 1, 1, 12, 12, 42, 42, 1, 1, 79] 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, 42])
total number of confs: 208
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037144 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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, 201, 201, 201, 138, 77, 77, 42, 27, 42, 42, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 201, 138, 77, 42, 42, 9, 9, 1, 1, 42, 42, 201] 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, 42])
total number of confs: 566
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037144 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 11, 43, 43, 79, 79, 43, 45, 113, 146, 201, 201, 201, 201, 201, 201, 201, 79, 79, 1, 1, 1, 2, 2, 2, 1, 1, 11, 43, 79, 79, 146, 146, 201, 201, 79, 79, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 568
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037144 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037144
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037144/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037144
Building REAL300000037145
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037145'
/scratch/stefan/7769618/working/building/REAL300000037145 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037145

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037145/0 /scratch/stefan/7769618/working/building/REAL300000037145 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/151
`/scratch/stefan/7769618/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1Cl)

`REAL300000037145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037145 none CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 6, 7, 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, 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, 31, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 31, 11, 2, 1, 1, 1, 1, 1, 56] 112
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, 38, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 118
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: REAL300000037145 none CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 6, 7, 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, 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: [1, 1, 1, 1, 1, 1, 11, 31, 31, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 2, 2, 2, 1, 1, 11, 30, 112, 56, 56, 56, 56, 56, 1] 112
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 212
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037145 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037145
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037145/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037145
Building REAL300000037146
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037146'
/scratch/stefan/7769618/working/building/REAL300000037146 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037146

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037146/0 /scratch/stefan/7769618/working/building/REAL300000037146 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/152
`/scratch/stefan/7769618/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1Cl)

`REAL300000037146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037146 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 52, 79, 79, 26, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 23, 23, 5, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 25, 5, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 79] 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, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037146 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 133, 139, 139, 61, 19, 15, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 139, 139, 139, 139, 139, 139, 139, 139, 61, 15, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 139] 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, 44])
total number of confs: 329
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037146 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 51, 51, 79, 79, 53, 79, 139, 139, 139, 139, 139, 201, 201, 201, 139, 79, 79, 1, 1, 1, 2, 2, 2, 1, 1, 11, 51, 79, 79, 139, 139, 139, 201, 201, 139, 79, 79, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 715
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037146 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037146
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037146/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037146
Building REAL300000037147
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037147'
/scratch/stefan/7769618/working/building/REAL300000037147 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037147

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037147/0 /scratch/stefan/7769618/working/building/REAL300000037147 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/153
`/scratch/stefan/7769618/working/3D/153' -> `0.mol2'
Preparing input files

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

`REAL300000037147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037147 none CCOC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 72, 32, 31, 31, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 109, 187, 195, 195, 101, 101, 101, 101, 101, 32, 10, 6, 1, 1, 2, 2, 2, 1, 31, 31, 187, 187] 201
rigid atoms, others: [33, 34, 38, 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, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 814
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037147 none CCOC1=CC(C=NNC2=CC=C(C)C(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', 'C.ar', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 32, 32, 25, 32, 32, 32, 32, 1, 1, 1, 1, 9, 36, 57, 57, 16, 16, 16, 16, 16, 1, 6, 12, 32, 32, 32, 32, 32, 31, 1, 1, 36, 36] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 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, 41, 42])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037147 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037147
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037147/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037147
Building REAL300000037148
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037148'
/scratch/stefan/7769618/working/building/REAL300000037148 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037148

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037148/0 /scratch/stefan/7769618/working/building/REAL300000037148 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/154
`/scratch/stefan/7769618/working/3D/154' -> `0.mol2'
Preparing input files

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

`REAL300000037148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037148 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 8, 32, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 32, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1] 85
rigid atoms, others: [1, 34, 35, 36, 37, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037148 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 56, 56, 56, 11, 1, 1, 2, 2, 2, 1, 85, 85, 85, 85] 85
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 133
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037148 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037148
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037148/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037148
Building REAL300000037149
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037149'
/scratch/stefan/7769618/working/building/REAL300000037149 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037149

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037149/0 /scratch/stefan/7769618/working/building/REAL300000037149 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/155
`/scratch/stefan/7769618/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1Cl)

`REAL300000037149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037149 none CC1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 54, 73, 73, 21, 7, 7, 1, 1, 1, 1, 1, 1, 7, 19, 31, 25, 1, 73, 73, 73, 73, 73, 73, 73, 73, 21, 7, 1, 1, 7, 7, 19, 19, 73] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 309
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037149 none CC1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 40, 40, 73, 73, 73, 73, 164, 201, 201, 189, 73, 1, 1, 1, 2, 2, 2, 1, 1, 10, 40, 73, 73, 164, 164, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 743
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037149 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037149
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037149/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037149
Building REAL300000037150
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037150'
/scratch/stefan/7769618/working/building/REAL300000037150 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037150

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037150/0 /scratch/stefan/7769618/working/building/REAL300000037150 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/156
`/scratch/stefan/7769618/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1Cl)

`REAL300000037150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037150 none CC1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 7, 1, 1, 1, 1, 1, 50] 50
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037150 none CC1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 1, 10, 28, 50, 50, 50, 50, 50, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037150 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037150
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037150/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037150
Building REAL300000037151
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037151'
/scratch/stefan/7769618/working/building/REAL300000037151 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037151

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037151/0 /scratch/stefan/7769618/working/building/REAL300000037151 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/157
`/scratch/stefan/7769618/working/3D/157' -> `0.mol2'
Preparing input files

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

`REAL300000037151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037151 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 20, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1] 42
rigid atoms, others: [1, 35, 36, 37, 38, 39, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 88
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037151 none CC(=NNC1=CC=C(C)C(Cl)=C1)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.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 34, 34, 34, 11, 1, 1, 2, 2, 2, 1, 42, 42, 42, 42, 42] 42
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 75
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037151 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037151
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037151/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037151
Building REAL300000037152
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037152'
/scratch/stefan/7769618/working/building/REAL300000037152 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037152

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037152/0 /scratch/stefan/7769618/working/building/REAL300000037152 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/158
`/scratch/stefan/7769618/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1Cl)

`REAL300000037152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037152 none CC1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 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, 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, 48, 49, 49, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 22, 8, 1, 1, 1, 1, 49] 49
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 15, 16, 20, 21, 22, 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: REAL300000037152 none CC1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 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, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 2, 2, 2, 1, 1, 13, 31, 49, 49, 49, 49, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037152 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037152
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037152/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037152
Building REAL300000037153
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037153'
/scratch/stefan/7769618/working/building/REAL300000037153 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037153

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037153/0 /scratch/stefan/7769618/working/building/REAL300000037153 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/159
`/scratch/stefan/7769618/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1Cl)

`REAL300000037153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037153 none CC1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 34, 34, 34, 35, 35, 35, 34, 34, 15, 5, 1, 1, 1, 1, 34] 35
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300000037153 none CC1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 32, 32, 34, 34, 34, 34, 34, 34, 35, 35, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 1, 10, 32, 34, 34, 34, 34, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037153 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037153
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037153/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037153
Building REAL300000037154
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037154'
/scratch/stefan/7769618/working/building/REAL300000037154 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037154

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037154/0 /scratch/stefan/7769618/working/building/REAL300000037154 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/160
`/scratch/stefan/7769618/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1Cl)

`REAL300000037154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037154 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 95, 95, 95, 95, 95, 95, 95, 20, 20, 20, 20, 20, 20, 20, 20, 8, 4, 1, 1, 1, 1, 31, 31, 95, 95, 20] 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, 42])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037154 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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, 201, 201, 142, 112, 112, 95, 95, 95, 95, 95, 95, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 142, 112, 95, 95, 95, 95, 9, 9, 1, 1, 201] 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, 42])
total number of confs: 443
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037154 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 7, 14, 14, 20, 20, 20, 20, 20, 20, 64, 144, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 14, 20, 20, 20, 20, 144, 144, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 538
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037154 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037154
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037154/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037154
Building REAL300000037155
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037155'
/scratch/stefan/7769618/working/building/REAL300000037155 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037155

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037155/0 /scratch/stefan/7769618/working/building/REAL300000037155 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/161
`/scratch/stefan/7769618/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1Cl)

`REAL300000037155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037155 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 16, 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, 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: [76, 76, 76, 76, 23, 7, 7, 1, 1, 1, 1, 1, 1, 9, 35, 53, 53, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 23, 7, 1, 1, 35, 35, 1, 76] 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, 35])
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: REAL300000037155 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 16, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 28, 28, 76, 76, 43, 75, 165, 201, 201, 201, 76, 76, 76, 1, 1, 1, 2, 2, 2, 1, 1, 8, 28, 76, 76, 201, 201, 76, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 576
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037155 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037155
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037155/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037155
Building REAL300000037156
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037156'
/scratch/stefan/7769618/working/building/REAL300000037156 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037156

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037156/0 /scratch/stefan/7769618/working/building/REAL300000037156 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/162
`/scratch/stefan/7769618/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1Cl)

`REAL300000037156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037156 none CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [25, 16, 25, 25, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 8, 4, 1, 1, 9, 17, 17, 1, 1, 25] 73
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, 39])
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: REAL300000037156 none CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 14, 14, 25, 25, 15, 15, 43, 43, 43, 67, 73, 73, 73, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 6, 14, 25, 25, 67, 73, 73, 25, 25, 1] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037156 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037156
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037156/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037156
Building REAL300000037157
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037157'
/scratch/stefan/7769618/working/building/REAL300000037157 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037157

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037157/0 /scratch/stefan/7769618/working/building/REAL300000037157 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/163
`/scratch/stefan/7769618/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1Cl)

`REAL300000037157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037157 none CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 1, 16, 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, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 36, 10, 1, 1, 1, 67] 67
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, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037157 none CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 1, 16, 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, 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
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, 10, 34, 34, 67, 67, 67, 67, 67, 67, 67, 67, 66, 67, 67, 67, 1, 1, 1, 2, 2, 2, 1, 1, 10, 34, 67, 66, 67, 1] 67
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037157 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037157
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037157/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037157
Building REAL300000037158
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037158'
/scratch/stefan/7769618/working/building/REAL300000037158 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037158

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037158/0 /scratch/stefan/7769618/working/building/REAL300000037158 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/164
`/scratch/stefan/7769618/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C)C(Cl)=C1)

`REAL300000037158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037158 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 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
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 38, 10, 1, 1, 2, 2, 2, 1] 53
rigid atoms, others: [35, 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, 34])
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: REAL300000037158 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C)C(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', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 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
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 53, 53, 53, 53, 53, 53, 53, 4, 4, 4, 1, 1, 1, 10, 26, 53, 53, 53, 53, 53, 53] 53
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 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: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037158 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037158
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037158/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037158
Building REAL300000037159
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037159'
/scratch/stefan/7769618/working/building/REAL300000037159 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037159

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037159/0 /scratch/stefan/7769618/working/building/REAL300000037159 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/165
`/scratch/stefan/7769618/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1Cl)

`REAL300000037159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037159 none CC1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 72, 19, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 12, 1, 1, 73, 73, 73, 73, 73, 73, 72, 73, 19, 4, 12, 12, 12, 12, 1, 1, 73] 201
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037159 none CC1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 97, 30, 30, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 201, 201, 201, 201, 201, 201, 201, 201, 97, 30, 1, 1, 1, 1, 12, 12, 201] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38])
total number of confs: 403
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037159 none CC1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 52, 52, 73, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 1, 1, 1, 2, 2, 2, 1, 1, 11, 52, 201, 201, 201, 201, 73, 73, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037159 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037159
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037159/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037159
Building REAL300000037160
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037160'
/scratch/stefan/7769618/working/building/REAL300000037160 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037160

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037160/0 /scratch/stefan/7769618/working/building/REAL300000037160 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/166
`/scratch/stefan/7769618/working/3D/166' -> `0.mol2'
Preparing input files

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

`REAL300000037160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037160 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 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, 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, 145, 54, 54, 54, 25, 54, 54, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 54, 54, 54, 54, 25, 6, 1, 1, 1, 1] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037160 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 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, 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: [90, 53, 90, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 54, 54, 26, 54, 54, 54, 53, 53, 1, 1, 1, 1, 5, 26, 54, 54, 26, 54] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 449
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037160 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037160
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037160/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037160
Building REAL300000037161
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037161'
/scratch/stefan/7769618/working/building/REAL300000037161 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037161

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037161/0 /scratch/stefan/7769618/working/building/REAL300000037161 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/167
`/scratch/stefan/7769618/working/3D/167' -> `0.mol2'
Preparing input files

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

`REAL300000037161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037161 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 33, 62, 62, 33, 62, 62, 62, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 33, 62, 62, 33, 62, 1, 1, 12, 12, 1, 1] 85
rigid atoms, others: [1, 34, 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, 32, 35, 36])
total number of confs: 207
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037161 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [44, 3, 44, 45, 77, 85, 85, 77, 85, 85, 85, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 45, 45, 77, 85, 85, 77, 85, 12, 12, 1, 1, 12, 12] 85
rigid atoms, others: [35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 275
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037161 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 62, 62, 27, 25, 85, 85, 85, 85, 85, 85, 85, 62, 62, 25, 25, 25, 5, 1, 1, 1, 1, 62, 62, 85, 85, 62, 62] 85
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 254
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037161 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037161
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037161/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037161
Building REAL300000037162
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037162'
/scratch/stefan/7769618/working/building/REAL300000037162 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037162

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037162/0 /scratch/stefan/7769618/working/building/REAL300000037162 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/168
`/scratch/stefan/7769618/working/3D/168' -> `0.mol2'
Preparing input files

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

`REAL300000037162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037162 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 41, 41, 41, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 131, 199, 201, 201, 80, 80, 80, 41, 14, 4, 1, 1, 1, 1, 41, 41, 199, 199] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 583
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037162 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 23, 41, 41, 23, 41, 41, 41, 1, 1, 1, 1, 9, 43, 68, 68, 3, 3, 3, 1, 7, 23, 41, 41, 23, 41, 1, 1, 43, 43] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 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, 32, 35, 36])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037162 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037162
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037162/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037162
Building REAL300000037163
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037163'
/scratch/stefan/7769618/working/building/REAL300000037163 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037163

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037163/0 /scratch/stefan/7769618/working/building/REAL300000037163 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/169
`/scratch/stefan/7769618/working/3D/169' -> `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=C2Cl)C=C1)

`REAL300000037163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037163 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [180, 178, 180, 104, 29, 29, 77, 76, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 178, 178, 77, 76, 28, 5, 1, 1, 1, 1, 77, 77] 180
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 32, 31])
total number of confs: 679
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: REAL300000037163 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [32, 16, 32, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 76, 76, 45, 76, 76, 76, 1, 1, 16, 16, 1, 1, 9, 43, 76, 76, 46, 76, 1, 1] 180
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 331
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037163 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037163
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037163/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037163
Building REAL300000037164
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037164'
/scratch/stefan/7769618/working/building/REAL300000037164 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037164

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037164/0 /scratch/stefan/7769618/working/building/REAL300000037164 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/170
`/scratch/stefan/7769618/working/3D/170' -> `0.mol2'
Preparing input files

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

`REAL300000037164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037164 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 68, 68, 41, 68, 68, 68, 1, 1, 1, 1, 1, 1, 6, 22, 39, 39, 1, 11, 11, 11, 41, 68, 68, 41, 68, 1, 1, 1, 22, 22, 1] 201
rigid atoms, others: [32, 1, 35, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 337
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: REAL300000037164 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 68, 68, 68, 68, 68, 144, 201, 201, 201, 68, 16, 16, 16, 4, 1, 1, 1, 1, 68, 68, 68, 201, 201, 68] 201
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])
total number of confs: 513
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037164 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037164
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037164/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037164
Building REAL300000037165
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037165'
/scratch/stefan/7769618/working/building/REAL300000037165 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037165

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037165/0 /scratch/stefan/7769618/working/building/REAL300000037165 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/171
`/scratch/stefan/7769618/working/3D/171' -> `0.mol2'
Preparing input files

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

`REAL300000037165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037165 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
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, 17, 25, 25, 17, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 17, 25, 25, 17, 25, 1, 1, 9, 17, 17, 1, 1] 64
rigid atoms, others: [1, 34, 38, 33, 11, 12, 13, 14, 15, 23, 24, 39] 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, 35, 36, 37])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037165 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 25, 25, 12, 12, 40, 40, 40, 58, 64, 64, 64, 25, 25, 12, 12, 12, 3, 1, 1, 1, 1, 25, 25, 58, 64, 64, 25, 25] 64
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 285
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037165 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037165
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037165/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037165
Building REAL300000037166
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037166'
/scratch/stefan/7769618/working/building/REAL300000037166 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037166

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037166/0 /scratch/stefan/7769618/working/building/REAL300000037166 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/172
`/scratch/stefan/7769618/working/3D/172' -> `0.mol2'
Preparing input files

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

`REAL300000037166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037166 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 1, 9, 9, 9, 9, 9, 1, 1] 37
rigid atoms, others: [1, 34, 35, 41, 42, 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, 36, 37, 38, 39, 40])
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: REAL300000037166 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 8, 8, 17, 17, 17, 37, 37, 37, 37, 37, 9, 9, 8, 8, 8, 3, 1, 1, 1, 1, 9, 9, 37, 37, 37, 37, 37, 9, 9] 37
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 137
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037166 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037166
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037166/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037166
Building REAL300000037167
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037167'
/scratch/stefan/7769618/working/building/REAL300000037167 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037167

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037167/0 /scratch/stefan/7769618/working/building/REAL300000037167 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/173
`/scratch/stefan/7769618/working/3D/173' -> `0.mol2'
Preparing input files

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

`REAL300000037167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037167 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 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]
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, 3, 1, 1, 5, 5, 5, 5, 1, 1] 9
rigid atoms, others: [1, 35, 36, 41, 42, 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, 37, 38, 39, 40])
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: REAL300000037167 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 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]
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, 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, 1, 3, 3, 9, 9, 9, 9, 3, 3] 9
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 42
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037167 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037167
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037167/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037167
Building REAL300000037168
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037168'
/scratch/stefan/7769618/working/building/REAL300000037168 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037168

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037168/0 /scratch/stefan/7769618/working/building/REAL300000037168 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/174
`/scratch/stefan/7769618/working/3D/174' -> `0.mol2'
Preparing input files

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

`REAL300000037168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037168 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 21, 23, 23, 21, 23, 23, 23, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 6, 6, 6, 21, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1] 43
rigid atoms, others: [1, 34, 33, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 81
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037168 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 15, 15, 43, 43, 43, 23, 23, 15, 15, 15, 5, 1, 1, 1, 1, 23, 23, 43, 43, 23, 23] 43
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 193
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037168 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037168
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037168/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037168
Building REAL300000037169
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037169'
/scratch/stefan/7769618/working/building/REAL300000037169 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037169

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037169/0 /scratch/stefan/7769618/working/building/REAL300000037169 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/175
`/scratch/stefan/7769618/working/3D/175' -> `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=C2Cl)C=C1)

`REAL300000037169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037169 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 174, 147, 108, 23, 23, 80, 79, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 175, 175, 147, 147, 80, 79, 22, 5, 1, 1, 1, 1, 80, 80] 175
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 643
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: REAL300000037169 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [43, 30, 37, 16, 3, 1, 1, 1, 1, 1, 1, 8, 8, 45, 79, 79, 45, 79, 79, 79, 1, 1, 30, 30, 16, 16, 1, 1, 8, 45, 79, 79, 50, 79, 1, 1] 175
rigid atoms, others: [34, 35, 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, 33])
total number of confs: 410
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037169 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037169
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037169/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037169
Building REAL300000037170
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037170'
/scratch/stefan/7769618/working/building/REAL300000037170 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037170

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037170/0 /scratch/stefan/7769618/working/building/REAL300000037170 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/176
`/scratch/stefan/7769618/working/3D/176' -> `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=C1Cl)

`REAL300000037170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037170 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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, 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, 141, 49, 49, 49, 26, 49, 49, 49, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 49, 49, 49, 26, 6, 1, 1, 1, 1] 201
rigid atoms, others: [32, 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: 623
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: REAL300000037170 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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, 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: [92, 56, 92, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 49, 49, 22, 49, 49, 49, 56, 56, 1, 1, 1, 4, 22, 49, 49, 22, 49] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 446
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037170 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037170
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037170/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037170
Building REAL300000037171
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037171'
/scratch/stefan/7769618/working/building/REAL300000037171 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037171

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037171/0 /scratch/stefan/7769618/working/building/REAL300000037171 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/177
`/scratch/stefan/7769618/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C(=O)[O-])

`REAL300000037171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037171 none CC(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 147, 55, 55, 55, 55, 55, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 19, 5, 1, 1, 1, 1, 55] 201
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 497
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: REAL300000037171 none CC(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 55, 55, 28, 55, 55, 55, 1, 31, 50, 50, 31, 31, 31, 31, 1, 1, 1, 7, 27, 55, 55, 29, 55, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 35, 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])
total number of confs: 337
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037171 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037171
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037171/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037171
Building REAL300000037172
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037172'
/scratch/stefan/7769618/working/building/REAL300000037172 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037172

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037172/0 /scratch/stefan/7769618/working/building/REAL300000037172 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/178
`/scratch/stefan/7769618/working/3D/178' -> `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=C2Cl)=C1)

`REAL300000037172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037172 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 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, 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, 193, 175, 110, 51, 51, 51, 51, 51, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 175, 175, 51, 51, 51, 17, 4, 1, 1, 1, 1, 51] 201
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 612
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: REAL300000037172 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 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, 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: [73, 49, 60, 30, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 51, 51, 30, 51, 51, 51, 1, 49, 49, 30, 30, 1, 1, 1, 8, 29, 51, 51, 30, 51, 1] 201
rigid atoms, others: [35, 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, 34])
total number of confs: 418
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037172 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037172
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037172/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037172
Building REAL300000037173
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037173'
/scratch/stefan/7769618/working/building/REAL300000037173 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037173

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037173/0 /scratch/stefan/7769618/working/building/REAL300000037173 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/179
`/scratch/stefan/7769618/working/3D/179' -> `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=C2Cl)=C1)

`REAL300000037173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037173 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
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, 8, 8, 26, 39, 39, 27, 39, 39, 39, 1, 16, 16, 16, 16, 6, 6, 1, 1, 1, 8, 26, 39, 39, 31, 39, 1] 98
rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 42] 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])
total number of confs: 168
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037173 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 98, 67, 63, 39, 39, 39, 39, 39, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 39, 98, 98, 98, 98, 67, 67, 39, 39, 39, 18, 6, 1, 1, 1, 1, 39] 98
rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 174
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037173 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 16, 16, 16, 16, 16, 53, 53, 86, 98, 98, 86, 98, 98, 98, 16, 1, 1, 1, 1, 5, 5, 16, 16, 16, 53, 85, 98, 98, 91, 98, 16] 98
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])
total number of confs: 287
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037173 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037173
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037173/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037173
Building REAL300000037174
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037174'
/scratch/stefan/7769618/working/building/REAL300000037174 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037174

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037174/0 /scratch/stefan/7769618/working/building/REAL300000037174 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/180
`/scratch/stefan/7769618/working/3D/180' -> `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=C2Cl)C=C1[N+](=O)[O-])

`REAL300000037174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037174 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 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, 3, 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, 20, 10, 10, 17, 17, 10, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 21, 21, 17, 17, 9, 3, 1, 1, 1, 1, 17] 21
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])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037174 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 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, 3, 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: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 13, 17, 17, 13, 17, 17, 17, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 13, 17, 17, 15, 17, 1] 21
rigid atoms, others: [34, 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, 33])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037174 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037174
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037174/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037174
Building REAL300000037175
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037175'
/scratch/stefan/7769618/working/building/REAL300000037175 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037175

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037175/0 /scratch/stefan/7769618/working/building/REAL300000037175 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/181
`/scratch/stefan/7769618/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1)

`REAL300000037175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037175 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 39, 39, 27, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 43, 71, 71, 43, 71, 71, 71, 1, 1, 27, 27, 27, 27, 7, 7, 1, 1, 10, 43, 71, 71, 43, 71, 1, 1, 27] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 40, 41, 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, 42])
total number of confs: 301
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037175 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 90, 72, 22, 22, 72, 71, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 90, 90, 72, 71, 21, 5, 1, 1, 1, 1, 72, 72, 201] 201
rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 482
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037175 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 99, 99, 176, 201, 201, 176, 201, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 99, 176, 201, 201, 182, 200, 26, 27, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 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])
total number of confs: 589
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037175 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037175
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037175/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037175
Building REAL300000037176
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037176'
/scratch/stefan/7769618/working/building/REAL300000037176 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037176

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037176/0 /scratch/stefan/7769618/working/building/REAL300000037176 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/182
`/scratch/stefan/7769618/working/3D/182' -> `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=C3Cl)=C2)=C1)

`REAL300000037176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037176 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
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, 1, 16, 1, 1, 7, 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, 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, 27, 27, 27, 26, 27, 27, 8, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 33, 33, 29, 33, 33, 33, 1, 27, 26, 27, 27, 8, 8, 1, 1, 1, 11, 27, 33, 33, 29, 33, 1, 27] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 41, 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, 40, 42])
total number of confs: 142
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037176 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
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, 1, 16, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 67, 55, 33, 33, 32, 33, 33, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 33, 201, 201, 201, 201, 67, 67, 32, 33, 33, 11, 5, 1, 1, 1, 1, 33, 201] 201
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 326
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037176 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
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, 1, 16, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 27, 27, 27, 27, 27, 137, 137, 185, 201, 201, 196, 201, 201, 201, 27, 1, 1, 1, 1, 9, 9, 27, 26, 27, 137, 185, 201, 201, 201, 201, 27, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 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])
total number of confs: 547
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037176 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037176
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037176/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037176
Building REAL300000037177
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037177'
/scratch/stefan/7769618/working/building/REAL300000037177 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037177

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037177/0 /scratch/stefan/7769618/working/building/REAL300000037177 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/183
`/scratch/stefan/7769618/working/3D/183' -> `0.mol2'
Preparing input files

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

`REAL300000037177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037177 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 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, 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, 131, 61, 61, 61, 61, 61, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 61, 61, 61, 24, 6, 1, 1, 1, 1, 61] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 527
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037177 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 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, 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: [53, 32, 53, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 32, 61, 61, 33, 61, 61, 61, 1, 32, 32, 1, 1, 1, 9, 32, 61, 61, 34, 61, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 354
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037177 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037177
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037177/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037177
Building REAL300000037178
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037178'
/scratch/stefan/7769618/working/building/REAL300000037178 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037178

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037178/0 /scratch/stefan/7769618/working/building/REAL300000037178 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/184
`/scratch/stefan/7769618/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)OC=C1)

`REAL300000037178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037178 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [15, 11, 15, 11, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 35, 35, 24, 35, 35, 35, 1, 1, 11, 11, 11, 5, 5, 1, 1, 6, 24, 35, 35, 24, 35, 1, 1, 11, 11] 67
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29, 37] 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, 38, 39])
total number of confs: 131
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037178 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 45, 35, 35, 35, 35, 35, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 67, 67, 67, 45, 45, 35, 35, 22, 6, 1, 1, 1, 1, 35, 35, 67, 67] 67
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39])
total number of confs: 134
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037178 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 11, 11, 11, 11, 38, 38, 55, 67, 67, 55, 67, 67, 67, 11, 11, 1, 1, 1, 5, 5, 11, 11, 38, 54, 67, 67, 55, 67, 11, 11, 1, 1] 67
rigid atoms, others: [1, 3, 4, 5, 38, 39, 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])
total number of confs: 198
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037178 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037178
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037178/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037178
Building REAL300000037179
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037179'
/scratch/stefan/7769618/working/building/REAL300000037179 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037179

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037179/0 /scratch/stefan/7769618/working/building/REAL300000037179 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/185
`/scratch/stefan/7769618/working/3D/185' -> `0.mol2'
Preparing input files

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

`REAL300000037179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037179 none COC1=CC=C(C=NNC2=CC=CC=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens 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, 46, 23, 46, 46, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 122, 190, 201, 201, 46, 63, 63, 63, 46, 46, 23, 6, 1, 1, 1, 1, 190, 190, 46] 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: 686
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037179 none COC1=CC=C(C=NNC2=CC=CC=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens 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, 20, 46, 46, 20, 46, 46, 46, 1, 1, 10, 43, 82, 82, 1, 3, 3, 3, 1, 1, 4, 20, 46, 46, 20, 46, 43, 43, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 22, 36, 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])
total number of confs: 417
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037179 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037179
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037179/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037179
Building REAL300000037180
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037180'
/scratch/stefan/7769618/working/building/REAL300000037180 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037180

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037180/0 /scratch/stefan/7769618/working/building/REAL300000037180 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/186
`/scratch/stefan/7769618/working/3D/186' -> `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=C2Cl)C=C1)

`REAL300000037180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037180 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 201, 115, 199, 198, 20, 20, 60, 59, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 59, 19, 3, 1, 1, 1, 1, 60, 60] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 21, 22, 23, 24, 25, 26, 31])
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: REAL300000037180 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 33, 57, 57, 33, 57, 57, 57, 1, 1, 1, 1, 7, 33, 57, 57, 34, 57, 1, 1] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037180 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037180
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037180/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037180
Building REAL300000037181
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037181'
/scratch/stefan/7769618/working/building/REAL300000037181 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037181

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037181/0 /scratch/stefan/7769618/working/building/REAL300000037181 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/187
`/scratch/stefan/7769618/working/3D/187' -> `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=C1Cl)

`REAL300000037181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037181 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 12, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 11, 5, 1, 1, 1, 1] 20
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25])
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: REAL300000037181 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 1, 1, 1, 1, 1, 8, 8, 16, 20, 20, 19, 20, 20, 20, 2, 2, 2, 1, 8, 16, 20, 20, 20, 20] 20
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])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037181 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037181
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037181/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037181
Building REAL300000037182
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037182'
/scratch/stefan/7769618/working/building/REAL300000037182 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037182

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037182/0 /scratch/stefan/7769618/working/building/REAL300000037182 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/188
`/scratch/stefan/7769618/working/3D/188' -> `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=C2Cl)C=C1Br)

`REAL300000037182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037182 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 17, 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, 159, 36, 36, 71, 71, 21, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 201, 201, 71, 71, 20, 3, 1, 1, 1, 1, 71] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32])
total number of confs: 551
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: REAL300000037182 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 17, 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: [72, 40, 72, 7, 1, 1, 1, 1, 1, 1, 8, 8, 36, 70, 70, 40, 71, 71, 71, 1, 1, 1, 40, 40, 1, 1, 8, 36, 71, 71, 70, 71, 1] 201
rigid atoms, others: [32, 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])
total number of confs: 488
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037182 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037182
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037182/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037182
Building REAL300000037183
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037183'
/scratch/stefan/7769618/working/building/REAL300000037183 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037183

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037183/0 /scratch/stefan/7769618/working/building/REAL300000037183 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/189
`/scratch/stefan/7769618/working/3D/189' -> `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=C2Cl)C=C1)

`REAL300000037183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037183 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 19, 5, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 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: REAL300000037183 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 22, 31, 31, 22, 31, 31, 31, 1, 1, 4, 4, 4, 1, 9, 22, 31, 31, 22, 31, 1, 1] 31
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 22, 23, 27] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 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/7769618/working/building/REAL300000037183 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037183
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037183/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037183
Building REAL300000037184
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037184'
/scratch/stefan/7769618/working/building/REAL300000037184 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037184

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037184/0 /scratch/stefan/7769618/working/building/REAL300000037184 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/190
`/scratch/stefan/7769618/working/3D/190' -> `0.mol2'
Preparing input files

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

`REAL300000037184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037184 none CCC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [16, 7, 1, 7, 7, 29, 39, 39, 33, 39, 39, 39, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 29, 39, 39, 34, 39, 1, 1, 1, 1] 44
rigid atoms, others: [32, 33, 2, 34, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 160
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: REAL300000037184 none CCC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [34, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 39, 39, 29, 37, 39, 39, 39, 39, 34, 34, 34, 34, 34, 5, 1, 1, 1, 1, 39, 39, 39, 39] 44
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 179
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037184 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037184
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037184/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037184
Building REAL300000037185
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037185'
/scratch/stefan/7769618/working/building/REAL300000037185 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037185

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037185/0 /scratch/stefan/7769618/working/building/REAL300000037185 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/191
`/scratch/stefan/7769618/working/3D/191' -> `0.mol2'
Preparing input files

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

`REAL300000037185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037185 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 29, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 29, 33, 33, 33, 33, 1, 1, 1, 2] 66
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 81
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: REAL300000037185 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 5, 1, 1, 1, 1, 33, 33, 33, 66] 66
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 128
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037185 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037185
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037185/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037185
Building REAL300000037186
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037186'
/scratch/stefan/7769618/working/building/REAL300000037186 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037186

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037186/0 /scratch/stefan/7769618/working/building/REAL300000037186 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/192
`/scratch/stefan/7769618/working/3D/192' -> `0.mol2'
Preparing input files

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

`REAL300000037186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037186 none CCC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
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: [29, 12, 1, 12, 12, 59, 77, 77, 65, 77, 77, 77, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 30, 30, 30, 29, 29, 59, 77, 77, 69, 77, 1, 1, 1] 86
rigid atoms, others: [32, 33, 2, 34, 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])
total number of confs: 308
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: REAL300000037186 none CCC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
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: [47, 24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 77, 77, 77, 77, 77, 77, 77, 77, 77, 48, 48, 48, 47, 47, 5, 1, 1, 1, 1, 77, 77, 77] 86
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])
total number of confs: 243
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037186 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037186
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037186/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037186
Building REAL300000037187
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037187'
/scratch/stefan/7769618/working/building/REAL300000037187 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037187

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037187/0 /scratch/stefan/7769618/working/building/REAL300000037187 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/193
`/scratch/stefan/7769618/working/3D/193' -> `0.mol2'
Preparing input files

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

`REAL300000037187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037187 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 13, 5, 1, 1, 1, 1, 15, 15] 15
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31])
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: REAL300000037187 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 13, 14, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 6, 12, 14, 15, 15, 15, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037187 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037187/1 /scratch/stefan/7769618/working/building/REAL300000037187 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/194
`/scratch/stefan/7769618/working/3D/194' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=C3Cl)=NNC2=C1)

`REAL300000037187.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037187/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037187 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 20, 21, 20, 20, 20, 20, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 11, 5, 1, 1, 1, 1, 20, 20] 21
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
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: REAL300000037187 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 14, 20, 20, 14, 20, 20, 20, 1, 1, 1, 1, 1, 1, 8, 14, 20, 20, 20, 20, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037187 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037187
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037187/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037187/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037187
Building REAL300000037188
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037188'
/scratch/stefan/7769618/working/building/REAL300000037188 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037188

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037188/0 /scratch/stefan/7769618/working/building/REAL300000037188 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/195
`/scratch/stefan/7769618/working/3D/195' -> `0.mol2'
Preparing input files

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

`REAL300000037188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037188 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 45, 67, 67, 55, 67, 67, 67, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 45, 67, 67, 55, 67, 1, 1, 1] 67
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 185
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037188 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [25, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 67, 67, 67, 67, 67, 67, 67, 67, 67, 26, 26, 26, 6, 1, 1, 1, 1, 67, 67, 67] 67
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037188 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037188
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037188/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037188
Building REAL300000037189
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037189'
/scratch/stefan/7769618/working/building/REAL300000037189 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037189

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037189/0 /scratch/stefan/7769618/working/building/REAL300000037189 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/196
`/scratch/stefan/7769618/working/3D/196' -> `0.mol2'
Preparing input files

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

`REAL300000037189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037189 none COC1=CC(C=NNC2=CC=CC=C2Cl)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [86, 50, 50, 50, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 117, 131, 131, 131, 86, 86, 86, 50, 20, 6, 1, 1, 1, 1, 50, 131, 131] 131
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])
total number of confs: 316
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: REAL300000037189 none COC1=CC(C=NNC2=CC=CC=C2Cl)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 24, 50, 50, 24, 50, 50, 50, 1, 1, 2, 2, 1, 1, 1, 9, 17, 24, 24, 3, 3, 3, 1, 7, 24, 50, 50, 24, 50, 1, 17, 17] 131
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 19, 20, 21, 36, 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, 37, 38])
total number of confs: 238
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037189 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037189
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037189/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037189
Building REAL300000037190
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037190'
/scratch/stefan/7769618/working/building/REAL300000037190 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037190

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037190/0 /scratch/stefan/7769618/working/building/REAL300000037190 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/197
`/scratch/stefan/7769618/working/3D/197' -> `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=C1Cl)

`REAL300000037190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037190 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [26, 23, 26, 32, 32, 32, 23, 23, 18, 23, 23, 23, 23, 23, 23, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 32, 32, 23, 23, 23, 18, 6, 1, 1, 1, 1] 32
rigid atoms, others: [36, 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])
total number of confs: 111
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: REAL300000037190 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 11, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 13, 23, 23, 13, 23, 23, 23, 4, 4, 4, 11, 11, 1, 1, 1, 4, 13, 23, 23, 13, 23] 32
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])
total number of confs: 139
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037190 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037190
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037190/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037190
Building REAL300000037191
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037191'
/scratch/stefan/7769618/working/building/REAL300000037191 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037191

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037191/0 /scratch/stefan/7769618/working/building/REAL300000037191 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/198
`/scratch/stefan/7769618/working/3D/198' -> `0.mol2'
Preparing input files

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

`REAL300000037191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037191 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 1, 6, 6, 34, 77, 77, 35, 77, 77, 77, 1, 1, 1, 1, 1, 9, 19, 19, 13, 13, 19, 19, 19, 19, 1, 1, 7, 7, 7, 34, 77, 77, 41, 77, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 35, 36, 41, 42, 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, 37, 38, 39, 40])
total number of confs: 328
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037191 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [76, 19, 76, 76, 185, 201, 201, 185, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 76, 76, 76, 185, 201, 201, 198, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 606
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037191 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [21, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 77, 77, 43, 77, 183, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 22, 22, 22, 6, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 77, 77] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 444
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037191 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037191
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037191/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037191
Building REAL300000037192
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037192'
/scratch/stefan/7769618/working/building/REAL300000037192 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037192

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037192/0 /scratch/stefan/7769618/working/building/REAL300000037192 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/199
`/scratch/stefan/7769618/working/3D/199' -> `0.mol2'
Preparing input files

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

`REAL300000037192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037192 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 38, 38, 38, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 127, 189, 193, 201, 195, 71, 71, 71, 38, 12, 4, 1, 1, 1, 1, 38, 38, 189, 189, 193, 193] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 597
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037192 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 20, 38, 38, 20, 38, 38, 38, 1, 1, 1, 1, 9, 37, 45, 82, 69, 4, 4, 4, 1, 7, 20, 38, 38, 20, 38, 1, 1, 37, 37, 45, 45] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 410
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037192 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037192
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037192/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037192
Building REAL300000037193
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037193'
/scratch/stefan/7769618/working/building/REAL300000037193 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037193

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037193/0 /scratch/stefan/7769618/working/building/REAL300000037193 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/200
`/scratch/stefan/7769618/working/3D/200' -> `0.mol2'
Preparing input files

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

`REAL300000037193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037193 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 17, 5, 1, 1, 1, 1, 20] 20
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 28])
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: REAL300000037193 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 14, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 14, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037193 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037193
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037193/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037193
Building REAL300000037194
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037194'
/scratch/stefan/7769618/working/building/REAL300000037194 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037194

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037194/0 /scratch/stefan/7769618/working/building/REAL300000037194 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/201
`/scratch/stefan/7769618/working/3D/201' -> `0.mol2'
Preparing input files

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

`REAL300000037194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037194 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 35, 51, 51, 47, 51, 51, 51, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 35, 51, 51, 51, 51, 1, 2, 2, 2, 2, 2, 2] 51
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 151
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037194 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 24, 24, 24, 5, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51] 51
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])
total number of confs: 85
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037194 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037194
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037194/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037194
Building REAL300000037195
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037195'
/scratch/stefan/7769618/working/building/REAL300000037195 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037195

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037195/0 /scratch/stefan/7769618/working/building/REAL300000037195 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/202
`/scratch/stefan/7769618/working/3D/202' -> `0.mol2'
Preparing input files

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

`REAL300000037195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037195 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 24, 26, 26, 24, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2] 26
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 85
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: REAL300000037195 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 5, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26] 26
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 50
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037195 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037195
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037195/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037195
Building REAL300000037196
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037196'
/scratch/stefan/7769618/working/building/REAL300000037196 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037196

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037196/0 /scratch/stefan/7769618/working/building/REAL300000037196 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/203
`/scratch/stefan/7769618/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1)C(=O)[O-])

`REAL300000037196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037196 none CC(OC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [159, 124, 24, 24, 74, 73, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 159, 161, 161, 159, 159, 159, 159, 74, 73, 23, 5, 1, 1, 1, 1, 74, 74] 161
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])
total number of confs: 511
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: REAL300000037196 none CC(OC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [22, 7, 1, 1, 1, 1, 1, 1, 8, 8, 42, 73, 73, 43, 73, 73, 74, 1, 1, 22, 31, 31, 22, 22, 22, 22, 1, 1, 8, 42, 73, 73, 43, 73, 1, 1] 161
rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 17, 18, 35, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 315
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037196 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037196
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037196/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037196
Building REAL300000037197
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037197'
/scratch/stefan/7769618/working/building/REAL300000037197 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037197

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037197/0 /scratch/stefan/7769618/working/building/REAL300000037197 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/204
`/scratch/stefan/7769618/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC=C2Cl)C2=CC=CC=C21)

`REAL300000037197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037197 none O=C([O-])CN1C=C(C=NNC2=CC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 38, 38, 38, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 38, 39, 39, 39, 39, 38, 71, 71, 38, 13, 5, 1, 1, 1, 1, 39, 39, 39, 39] 71
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037197 none O=C([O-])CN1C=C(C=NNC2=CC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [14, 8, 14, 1, 1, 1, 1, 1, 10, 10, 30, 39, 39, 31, 39, 38, 38, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 30, 39, 39, 34, 39, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037197 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037197/1 /scratch/stefan/7769618/working/building/REAL300000037197 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/205
`/scratch/stefan/7769618/working/3D/205' -> `1.mol2'
Preparing input files

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

`REAL300000037197.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037197/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037197 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 86, 86, 86, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 201, 201, 86, 28, 29, 1, 1, 1, 1, 86, 86, 86, 86] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 692
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037197 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 8, 14, 1, 1, 1, 1, 1, 9, 60, 60, 86, 86, 66, 86, 86, 86, 1, 1, 1, 1, 1, 1, 8, 8, 1, 9, 9, 86, 86, 73, 86, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037197 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037197
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037197/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037197/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037197
Building REAL300000037198
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037198'
/scratch/stefan/7769618/working/building/REAL300000037198 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037198

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037198/0 /scratch/stefan/7769618/working/building/REAL300000037198 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/206
`/scratch/stefan/7769618/working/3D/206' -> `0.mol2'
Preparing input files

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

`REAL300000037198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037198 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 25, 29, 29, 25, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 23, 37, 55, 75, 75, 1, 11, 11, 11, 25, 29, 29, 25, 29, 1, 1, 1, 23, 23, 37, 37, 55, 55, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 387
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: REAL300000037198 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 88, 133, 162, 201, 201, 201, 29, 8, 8, 8, 4, 1, 1, 1, 1, 29, 29, 29, 133, 133, 162, 162, 201, 201, 29] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 716
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037198 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037198
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037198/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037198
Building REAL300000037199
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037199'
/scratch/stefan/7769618/working/building/REAL300000037199 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037199

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037199/0 /scratch/stefan/7769618/working/building/REAL300000037199 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/207
`/scratch/stefan/7769618/working/3D/207' -> `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=C1Cl)

`REAL300000037199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037199 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 3, 21, 48, 53, 54, 54, 53, 54, 168, 201, 201, 201, 201, 54, 54, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 51, 51, 52, 53, 54, 54, 201, 201, 201, 201, 54, 54, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 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: 573
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037199 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 3, 1, 1, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1, 9, 37, 37, 54, 54, 37, 54, 54, 54, 9, 9, 9, 9, 4, 4, 3, 3, 1, 1, 27, 27, 27, 27, 1, 1, 54, 54, 37, 54] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 271
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037199 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037199
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037199/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037199
Building REAL300000037200
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037200'
/scratch/stefan/7769618/working/building/REAL300000037200 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037200

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037200/0 /scratch/stefan/7769618/working/building/REAL300000037200 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/208
`/scratch/stefan/7769618/working/3D/208' -> `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=C1Cl)

`REAL300000037200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037200 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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: [24, 4, 24, 51, 56, 60, 60, 56, 60, 137, 201, 201, 201, 60, 60, 4, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 54, 54, 55, 56, 60, 60, 201, 201, 60, 60, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 691
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: REAL300000037200 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 25, 40, 40, 1, 1, 11, 50, 50, 60, 60, 50, 60, 60, 60, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 25, 25, 1, 1, 60, 60, 53, 60] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41])
total number of confs: 270
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037200 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037200
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037200/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037200
Building REAL300000037201
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037201'
/scratch/stefan/7769618/working/building/REAL300000037201 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037201

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037201/0 /scratch/stefan/7769618/working/building/REAL300000037201 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/209
`/scratch/stefan/7769618/working/3D/209' -> `0.mol2'
Preparing input files

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

`REAL300000037201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037201 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 56, 56, 35, 56, 56, 56, 1, 1, 1, 1, 1, 1, 11, 27, 27, 41, 41, 1, 11, 11, 11, 35, 56, 56, 35, 56, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [32, 1, 38, 33, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 304
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037201 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 56, 56, 56, 56, 56, 153, 201, 201, 201, 201, 56, 17, 17, 17, 4, 1, 1, 1, 1, 56, 56, 56, 201, 201, 201, 201, 56] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 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: 483
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037201 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037201
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037201/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037201
Building REAL300000037202
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037202'
/scratch/stefan/7769618/working/building/REAL300000037202 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037202

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037202/0 /scratch/stefan/7769618/working/building/REAL300000037202 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/210
`/scratch/stefan/7769618/working/3D/210' -> `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=C1Cl)

`REAL300000037202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037202 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 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, 52, 58, 63, 63, 58, 63, 187, 201, 201, 201, 198, 63, 63, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 55, 55, 57, 58, 63, 63, 201, 201, 201, 201, 63, 63, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 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: 497
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: REAL300000037202 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 4, 1, 1, 1, 1, 1, 1, 6, 20, 20, 31, 27, 1, 1, 11, 47, 47, 63, 63, 47, 63, 63, 63, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 20, 20, 20, 20, 1, 1, 63, 63, 49, 63] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 261
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037202 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037202
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037202/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037202
Building REAL300000037203
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037203'
/scratch/stefan/7769618/working/building/REAL300000037203 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037203

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037203/0 /scratch/stefan/7769618/working/building/REAL300000037203 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/211
`/scratch/stefan/7769618/working/3D/211' -> `0.mol2'
Preparing input files

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

`REAL300000037203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037203 none CCC(=NNC1=CC=CC=C1Cl)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 1, 6, 6, 21, 22, 22, 21, 22, 22, 22, 1, 1, 1, 1, 1, 6, 10, 26, 29, 46, 50, 52, 1, 1, 9, 9, 9, 9, 9, 21, 22, 22, 21, 22, 1, 1, 10, 10, 25, 25, 30, 30, 45, 45, 1, 1] 201
rigid atoms, others: [2, 36, 37, 12, 13, 14, 15, 16, 46, 24, 25, 47] 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, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 301
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037203 none CCC(=NNC1=CC=CC=C1Cl)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 7, 8, 61, 81, 121, 132, 167, 171, 171, 22, 22, 12, 12, 12, 11, 11, 2, 1, 1, 1, 1, 22, 22, 78, 79, 121, 121, 132, 132, 167, 167, 22, 22] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 715
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037203 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037203
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037203/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037203
Building REAL300000037204
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037204'
/scratch/stefan/7769618/working/building/REAL300000037204 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037204

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037204/0 /scratch/stefan/7769618/working/building/REAL300000037204 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/212
`/scratch/stefan/7769618/working/3D/212' -> `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=C2Cl)C1)

`REAL300000037204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037204 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 18, 18, 16, 18, 18, 18, 4, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 16, 18, 4, 4] 18
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])
total number of confs: 38
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037204 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [16, 13, 16, 13, 13, 18, 18, 15, 18, 18, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 18, 18, 13, 13, 13, 1, 1, 1, 1, 13, 13] 18
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 63
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037204 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 11, 11, 13, 13, 11, 13, 13, 13, 1, 4, 4, 4, 4, 4, 1, 1, 1, 13, 13, 11, 13, 1, 1] 18
rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 39
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037204 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037204
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037204/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037204
Building REAL300000037205
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037205'
/scratch/stefan/7769618/working/building/REAL300000037205 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037205

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037205/0 /scratch/stefan/7769618/working/building/REAL300000037205 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/213
`/scratch/stefan/7769618/working/3D/213' -> `0.mol2'
Preparing input files

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

`REAL300000037205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037205 none CC(N=NC1=CC=CC=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 17, 17, 29, 29, 17, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 29, 29, 22, 29, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 41
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
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: REAL300000037205 none CC(N=NC1=CC=CC=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 29, 29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 20, 20, 20, 20, 1, 1, 1, 1, 29, 29, 41, 41, 29, 29, 29, 29, 29, 29] 41
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037205 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037205
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037205/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037205
Building REAL300000037206
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037206'
/scratch/stefan/7769618/working/building/REAL300000037206 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037206

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037206/0 /scratch/stefan/7769618/working/building/REAL300000037206 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/214
`/scratch/stefan/7769618/working/3D/214' -> `0.mol2'
Preparing input files

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

`REAL300000037206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037206 none COC1=CC(C(C)=NNC2=CC=CC=C2Cl)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 28, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 92, 166, 176, 201, 201, 201, 47, 47, 47, 28, 7, 7, 7, 2, 1, 1, 1, 1, 28, 28, 166, 166, 176, 176, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 712
number of broken/clashed sets: 115
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037206 none COC1=CC(C(C)=NNC2=CC=CC=C2Cl)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 8, 24, 28, 40, 57, 57, 3, 3, 3, 1, 11, 11, 11, 28, 28, 28, 28, 28, 1, 1, 24, 24, 28, 28, 40, 40] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 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, 40, 41, 42, 43, 44, 45])
total number of confs: 309
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037206 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037206
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037206/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037206
Building REAL300000037207
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037207'
/scratch/stefan/7769618/working/building/REAL300000037207 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037207

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037207/0 /scratch/stefan/7769618/working/building/REAL300000037207 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/215
`/scratch/stefan/7769618/working/3D/215' -> `0.mol2'
Preparing input files

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

`REAL300000037207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037207 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 21, 21, 19, 21, 21, 21, 9, 1, 1, 1, 1, 9, 9, 9, 21, 21, 19, 21, 9, 9] 21
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])
total number of confs: 49
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037207 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [11, 10, 11, 10, 10, 21, 21, 21, 21, 21, 21, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 10, 10] 21
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 43
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037207 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 7, 7, 9, 9, 7, 10, 10, 10, 1, 9, 9, 9, 9, 1, 1, 1, 10, 10, 7, 10, 1, 1] 21
rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 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, 33])
total number of confs: 43
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037207 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037207
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037207/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037207
Building REAL300000037208
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037208'
/scratch/stefan/7769618/working/building/REAL300000037208 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037208

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037208/0 /scratch/stefan/7769618/working/building/REAL300000037208 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/216
`/scratch/stefan/7769618/working/3D/216' -> `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=C2Cl)C1)

`REAL300000037208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037208 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 21, 21, 19, 21, 21, 21, 9, 1, 1, 1, 1, 9, 9, 9, 21, 21, 19, 21, 9, 9] 21
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])
total number of confs: 49
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037208 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [11, 10, 11, 10, 10, 21, 21, 21, 21, 21, 21, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 10, 10] 21
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 43
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037208 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 7, 7, 9, 9, 7, 10, 10, 10, 1, 9, 9, 9, 9, 1, 1, 1, 10, 10, 7, 10, 1, 1] 21
rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 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, 33])
total number of confs: 43
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037208 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037208
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037208/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037208
Building REAL300000037209
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037209'
/scratch/stefan/7769618/working/building/REAL300000037209 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037209

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037209/0 /scratch/stefan/7769618/working/building/REAL300000037209 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/217
`/scratch/stefan/7769618/working/3D/217' -> `0.mol2'
Preparing input files

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

`REAL300000037209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037209 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1] 9
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 16
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: REAL300000037209 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 9, 9, 5, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9] 9
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, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 31
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037209 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037209
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037209/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037209
Building REAL300000037210
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037210'
/scratch/stefan/7769618/working/building/REAL300000037210 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037210

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037210/0 /scratch/stefan/7769618/working/building/REAL300000037210 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/218
`/scratch/stefan/7769618/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000037210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037210 none CC(=NNC1=CC=CC=C1Cl)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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 73, 73, 41, 73, 73, 73, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 74, 74, 9, 9, 9, 41, 73, 73, 41, 73, 1, 1, 1, 44, 44] 201
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 467
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: REAL300000037210 none CC(=NNC1=CC=CC=C1Cl)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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 73, 73, 73, 20, 73, 73, 73, 153, 201, 201, 201, 20, 20, 20, 6, 1, 1, 1, 1, 73, 73, 73, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 643
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037210 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037210
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037210/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037210
Building REAL300000037211
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037211'
/scratch/stefan/7769618/working/building/REAL300000037211 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037211

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037211/0 /scratch/stefan/7769618/working/building/REAL300000037211 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/219
`/scratch/stefan/7769618/working/3D/219' -> `0.mol2'
Preparing input files

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

`REAL300000037211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037211 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC=C1Cl)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 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: [52, 52, 52, 52, 52, 52, 52, 52, 33, 6, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 64, 64, 64, 52, 52, 52, 52, 52, 52, 33, 33, 33, 33, 1, 1, 1, 1, 64, 64] 64
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
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: REAL300000037211 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC=C1Cl)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 32, 32, 52, 52, 38, 52, 52, 52, 1, 1, 2, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 52, 52, 47, 52, 2, 2] 64
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, 40])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037211 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037211
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037211/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037211
Building REAL300000037212
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037212'
/scratch/stefan/7769618/working/building/REAL300000037212 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037212

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037212/0 /scratch/stefan/7769618/working/building/REAL300000037212 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/220
`/scratch/stefan/7769618/working/3D/220' -> `0.mol2'
Preparing input files

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

`REAL300000037212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037212 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 17, 5, 1, 1, 1, 1] 27
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037212 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 23, 27, 27, 23, 27, 27, 27, 2, 2, 2, 1, 2, 2, 2, 1, 11, 23, 27, 27, 27, 27] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037212 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037212
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037212/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037212
Building REAL300000037213
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037213'
/scratch/stefan/7769618/working/building/REAL300000037213 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037213

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037213/0 /scratch/stefan/7769618/working/building/REAL300000037213 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/221
`/scratch/stefan/7769618/working/3D/221' -> `0.mol2'
Preparing input files

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

`REAL300000037213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037213 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 14, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 13, 5, 1, 1, 1, 1] 17
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24])
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: REAL300000037213 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 17, 11, 17, 17, 17, 1, 1, 1, 1, 1, 5, 11, 17, 17, 13, 17] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 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/7769618/working/building/REAL300000037213 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037213
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037213/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037213
Building REAL300000037214
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037214'
/scratch/stefan/7769618/working/building/REAL300000037214 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037214

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037214/0 /scratch/stefan/7769618/working/building/REAL300000037214 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/222
`/scratch/stefan/7769618/working/3D/222' -> `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=C1Cl)

`REAL300000037214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037214 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
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, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 10, 11, 11, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1] 11
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 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: REAL300000037214 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
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, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 6, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 10, 11] 11
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, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037214 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037214
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037214/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037214
Building REAL300000037215
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037215'
/scratch/stefan/7769618/working/building/REAL300000037215 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037215

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037215/0 /scratch/stefan/7769618/working/building/REAL300000037215 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/223
`/scratch/stefan/7769618/working/3D/223' -> `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=C2Cl)=C1)C1=CC=CC=C1)

`REAL300000037215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037215 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 192, 201, 87, 23, 23, 23, 23, 23, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 23, 192, 201, 201, 192, 201, 201, 192, 23, 23, 23, 10, 4, 1, 1, 1, 1, 23, 201, 201, 192, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 670
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037215 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 1, 4, 11, 52, 52, 52, 52, 52, 148, 148, 198, 201, 201, 198, 201, 201, 201, 52, 1, 1, 1, 1, 1, 1, 4, 52, 52, 52, 148, 198, 201, 201, 198, 201, 52, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 38, 39, 40, 41, 42, 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])
total number of confs: 525
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037215 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2Cl)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 37, 52, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 23, 23, 19, 23, 23, 23, 1, 37, 52, 52, 37, 52, 52, 37, 1, 1, 1, 6, 18, 23, 23, 19, 23, 1, 52, 52, 37, 52, 52] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 28, 29, 30, 37] 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, 36, 38, 39, 40, 41, 42])
total number of confs: 321
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037215 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037215
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037215/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037215
Building REAL300000037216
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037216'
/scratch/stefan/7769618/working/building/REAL300000037216 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037216

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037216/0 /scratch/stefan/7769618/working/building/REAL300000037216 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/224
`/scratch/stefan/7769618/working/3D/224' -> `0.mol2'
Preparing input files

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

`REAL300000037216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037216 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 56, 106, 106, 56, 106, 106, 106, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 21, 21, 11, 11, 11, 56, 106, 106, 66, 106, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 138
rigid atoms, others: [32, 1, 34, 33, 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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 419
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: REAL300000037216 none CC(=NNC1=CC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 106, 106, 106, 106, 106, 106, 106, 106, 106, 138, 138, 138, 24, 24, 24, 5, 1, 1, 1, 1, 106, 106, 106, 138, 138, 138, 138, 138, 138, 138] 138
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 206
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037216 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037216
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037216/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037216
Building REAL300000037217
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037217'
/scratch/stefan/7769618/working/building/REAL300000037217 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037217

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037217/0 /scratch/stefan/7769618/working/building/REAL300000037217 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/225
`/scratch/stefan/7769618/working/3D/225' -> `0.mol2'
Preparing input files

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

`REAL300000037217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037217 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC=C1Cl)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 3, 1, 1, 1, 1, 5, 5, 5, 5] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 32, 29, 30, 31])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037217 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC=C1Cl)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1] 6
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037217 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037217
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037217/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037217
Building REAL300000037218
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037218'
/scratch/stefan/7769618/working/building/REAL300000037218 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037218

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037218/0 /scratch/stefan/7769618/working/building/REAL300000037218 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/226
`/scratch/stefan/7769618/working/3D/226' -> `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=C3Cl)C=C2)C=C1)

`REAL300000037218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037218 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 15, 17, 17, 15, 17, 17, 17, 1, 1, 3, 3, 3, 3, 1, 1, 4, 15, 17, 17, 17, 17, 1, 1, 3, 3] 21
rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 35, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 66
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037218 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 15, 15, 16, 16, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 21, 21, 21, 21, 16, 16, 15, 5, 1, 1, 1, 1, 16, 16, 21, 21] 21
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 42
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037218 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 19, 21, 21, 19, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 8, 19, 21, 21, 21, 21, 3, 3, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 78
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037218 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037218
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037218/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037218
Building REAL300000037219
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037219'
/scratch/stefan/7769618/working/building/REAL300000037219 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037219

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037219/0 /scratch/stefan/7769618/working/building/REAL300000037219 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/227
`/scratch/stefan/7769618/working/3D/227' -> `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=CC=C3Cl)C2=C1)

`REAL300000037219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037219 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 15, 15, 15, 12, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 15, 15, 15, 15, 11, 5, 1, 1, 1, 1, 14] 15
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 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: REAL300000037219 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 14, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 6, 12, 14, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037219 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037219
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037219/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037219
Building REAL300000037220
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037220'
/scratch/stefan/7769618/working/building/REAL300000037220 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037220

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037220/0 /scratch/stefan/7769618/working/building/REAL300000037220 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/228
`/scratch/stefan/7769618/working/3D/228' -> `0.mol2'
Preparing input files

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

`REAL300000037220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037220 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [90, 56, 56, 56, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 101, 122, 122, 132, 132, 90, 90, 90, 56, 19, 6, 1, 1, 1, 1, 56, 122, 122, 122, 122] 132
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 366
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037220 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 32, 56, 56, 33, 56, 56, 56, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 4, 4, 4, 1, 9, 32, 56, 56, 33, 56, 1, 14, 14, 14, 14] 132
rigid atoms, others: [19, 1, 2, 3, 4, 5, 15, 16, 17, 18, 35, 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, 36, 37, 38, 39])
total number of confs: 241
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037220 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037220
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037220/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037220
Building REAL300000037221
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037221'
/scratch/stefan/7769618/working/building/REAL300000037221 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037221

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037221/0 /scratch/stefan/7769618/working/building/REAL300000037221 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/229
`/scratch/stefan/7769618/working/3D/229' -> `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=CC=C2Cl)=C1)

`REAL300000037221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037221 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 16, 5, 1, 1, 1, 1, 37] 37
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 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: REAL300000037221 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 8, 8, 25, 37, 37, 35, 37, 37, 37, 1, 8, 25, 37, 37, 35, 37, 1] 37
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037221 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037221
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037221/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037221
Building REAL300000037222
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037222'
/scratch/stefan/7769618/working/building/REAL300000037222 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037222

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037222/0 /scratch/stefan/7769618/working/building/REAL300000037222 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/230
`/scratch/stefan/7769618/working/3D/230' -> `0.mol2'
Preparing input files

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

`REAL300000037222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037222 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 21, 25, 25, 24, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2] 25
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 70
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037222 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 25, 25, 24, 25, 25, 25, 25, 25, 25, 20, 20, 20, 5, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25] 25
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 52
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037222 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037222
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037222/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037222
Building REAL300000037223
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037223'
/scratch/stefan/7769618/working/building/REAL300000037223 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037223

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037223/0 /scratch/stefan/7769618/working/building/REAL300000037223 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/231
`/scratch/stefan/7769618/working/3D/231' -> `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=C3Cl)O2)=CC=C1O)

`REAL300000037223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
246  conformations in input
total number of sets (complete confs): 246
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 25, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 32, 47, 47, 36, 47, 47, 47, 1, 12, 12, 12, 12, 12, 1, 1, 9, 32, 47, 47, 47, 47, 12, 12, 24] 246
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])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
246  conformations in input
total number of sets (complete confs): 246
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 47, 47, 47, 47, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 47, 123, 123, 123, 123, 123, 47, 47, 23, 5, 1, 1, 1, 1, 123, 123, 246] 246
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 422
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
246  conformations in input
total number of sets (complete confs): 246
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 49, 49, 105, 123, 123, 119, 123, 123, 123, 12, 1, 1, 1, 1, 1, 12, 12, 49, 105, 123, 123, 123, 123, 1, 1, 2] 246
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 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, 33, 36])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037223 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037223/1 /scratch/stefan/7769618/working/building/REAL300000037223 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/232
`/scratch/stefan/7769618/working/3D/232' -> `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=C3Cl)O2)=CC=C1O)

`REAL300000037223.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037223/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [16, 13, 16, 12, 12, 1, 1, 1, 1, 1, 1, 8, 64, 64, 70, 70, 64, 70, 70, 71, 1, 12, 12, 12, 12, 12, 1, 1, 8, 8, 70, 70, 64, 71, 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, 36])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 71, 71, 71, 71, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 71, 71, 15, 15, 1, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 692
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037223 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3Cl)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 73, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 72, 73, 201, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 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, 33, 36])
total number of confs: 421
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037223 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037223
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037223/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037223/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037223
Building REAL300000037224
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037224'
/scratch/stefan/7769618/working/building/REAL300000037224 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037224

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037224/0 /scratch/stefan/7769618/working/building/REAL300000037224 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/233
`/scratch/stefan/7769618/working/3D/233' -> `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=C1Cl)

`REAL300000037224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037224 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1] 8
rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 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: REAL300000037224 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 6, 8, 8, 6, 8, 8, 8, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 6, 8, 8, 8, 8] 8
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])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037224 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037224
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037224/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037224
Building REAL300000037225
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037225'
/scratch/stefan/7769618/working/building/REAL300000037225 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037225

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037225/0 /scratch/stefan/7769618/working/building/REAL300000037225 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/234
`/scratch/stefan/7769618/working/3D/234' -> `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=C3Cl)S2)C=C1)

`REAL300000037225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037225 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 28, 36, 36, 34, 36, 36, 36, 1, 7, 7, 7, 7, 1, 1, 8, 28, 37, 37, 36, 36, 7, 7] 47
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])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037225 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 47, 37, 47, 47, 37, 37, 37, 36, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 47, 47, 47, 47, 37, 36, 23, 5, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 146
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037225 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 37, 45, 45, 44, 45, 45, 45, 7, 1, 1, 1, 1, 7, 7, 22, 37, 45, 45, 45, 45, 1, 1] 45
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037225 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037225
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037225/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037225
Building REAL300000037226
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037226'
/scratch/stefan/7769618/working/building/REAL300000037226 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037226

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037226/0 /scratch/stefan/7769618/working/building/REAL300000037226 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/235
`/scratch/stefan/7769618/working/3D/235' -> `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=C3Cl)S2)=C1)

`REAL300000037226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037226 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 34, 55, 55, 34, 55, 55, 55, 1, 13, 12, 13, 13, 1, 1, 8, 34, 55, 55, 41, 55, 13] 100
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])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037226 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 55, 55, 55, 55, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 55, 100, 100, 100, 100, 55, 55, 26, 6, 1, 1, 1, 1, 100] 100
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 159
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037226 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 51, 51, 83, 100, 100, 84, 100, 100, 100, 13, 1, 1, 1, 1, 13, 13, 51, 83, 100, 100, 100, 100, 1] 100
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037226 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037226
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037226/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037226
Building REAL300000037227
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037227'
/scratch/stefan/7769618/working/building/REAL300000037227 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037227

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037227/0 /scratch/stefan/7769618/working/building/REAL300000037227 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/236
`/scratch/stefan/7769618/working/3D/236' -> `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=CC=C1Cl)

`REAL300000037227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037227 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 39, 39, 39, 19, 5, 1, 1, 1, 1] 40
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037227 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 39, 39, 33, 39, 39, 39, 4, 4, 4, 1, 1, 1, 10, 29, 39, 39, 33, 39] 40
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037227 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037227
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037227/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037227
Building REAL300000037228
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037228'
/scratch/stefan/7769618/working/building/REAL300000037228 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037228

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037228/0 /scratch/stefan/7769618/working/building/REAL300000037228 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/237
`/scratch/stefan/7769618/working/3D/237' -> `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=C3Cl)C2=C1)

`REAL300000037228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037228 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 11, 6, 1, 1, 1, 1, 14] 14
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037228 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 12, 14, 14, 12, 14, 14, 14, 1, 1, 1, 1, 1, 7, 12, 14, 14, 12, 14, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037228 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037228
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037228/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037228
Building REAL300000037229
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037229'
/scratch/stefan/7769618/working/building/REAL300000037229 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037229

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037229/0 /scratch/stefan/7769618/working/building/REAL300000037229 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/238
`/scratch/stefan/7769618/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3Cl)C2=C1)

`REAL300000037229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037229 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 9] 9
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 16
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: REAL300000037229 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 9, 9, 5, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 5, 9, 1] 9
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, 34] set([32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31])
total number of confs: 25
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037229 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037229
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037229/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037229
Building REAL300000037230
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037230'
/scratch/stefan/7769618/working/building/REAL300000037230 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037230

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037230/0 /scratch/stefan/7769618/working/building/REAL300000037230 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/239
`/scratch/stefan/7769618/working/3D/239' -> `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=C2Cl)=C1)

`REAL300000037230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037230 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 14, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 13, 5, 1, 1, 1, 1, 24] 24
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 28])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037230 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 24, 24, 24, 24, 24, 24, 1, 1, 1, 8, 22, 24, 24, 24, 24, 1] 24
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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/7769618/working/building/REAL300000037230 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037230
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037230/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037230
Building REAL300000037231
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037231'
/scratch/stefan/7769618/working/building/REAL300000037231 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037231

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037231/0 /scratch/stefan/7769618/working/building/REAL300000037231 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/240
`/scratch/stefan/7769618/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1C(=O)[O-])

`REAL300000037231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037231 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 62, 62, 62, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 70, 70, 70, 70, 70, 62, 22, 6, 1, 1, 1, 1, 62, 62] 70
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
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: REAL300000037231 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 29, 62, 62, 30, 62, 62, 62, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 6, 29, 62, 62, 32, 62, 1, 1] 70
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037231 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037231
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037231/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037231
Building REAL300000037232
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037232'
/scratch/stefan/7769618/working/building/REAL300000037232 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037232

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037232/0 /scratch/stefan/7769618/working/building/REAL300000037232 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/241
`/scratch/stefan/7769618/working/3D/241' -> `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=CC=C2Cl)C(F)=C1)

`REAL300000037232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037232 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 14, 14, 14, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 12, 6, 1, 1, 1, 1, 14] 14
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28])
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: REAL300000037232 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 9, 14, 14, 10, 14, 14, 14, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037232 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037232
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037232/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037232
Building REAL300000037233
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037233'
/scratch/stefan/7769618/working/building/REAL300000037233 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037233

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037233/0 /scratch/stefan/7769618/working/building/REAL300000037233 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/242
`/scratch/stefan/7769618/working/3D/242' -> `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=C2Cl)=C1)

`REAL300000037233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037233 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 36, 12, 5, 1, 1, 1, 1, 18] 36
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 29])
total number of confs: 68
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: REAL300000037233 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 18, 18, 15, 18, 18, 18, 1, 1, 2, 8, 15, 18, 18, 18, 18, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 62
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037233 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037233/1 /scratch/stefan/7769618/working/building/REAL300000037233 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/243
`/scratch/stefan/7769618/working/3D/243' -> `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=C2Cl)=C1)

`REAL300000037233.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037233/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037233 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 3, 1, 1, 1, 1, 8] 8
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 28])
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: REAL300000037233 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 8, 8, 6, 8, 8, 8, 1, 1, 4, 6, 8, 8, 8, 8, 1] 8
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: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037233 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037233
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037233/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037233/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037233
Building REAL300000037234
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037234'
/scratch/stefan/7769618/working/building/REAL300000037234 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037234

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037234/0 /scratch/stefan/7769618/working/building/REAL300000037234 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/244
`/scratch/stefan/7769618/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)O1)

`REAL300000037234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037234 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [31, 30, 31, 30, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 85, 85, 44, 85, 85, 85, 1, 1, 30, 30, 30, 7, 7, 1, 1, 10, 44, 85, 85, 52, 85, 1, 1] 177
rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 39, 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])
total number of confs: 331
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037234 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 177, 177, 177, 177, 138, 86, 27, 27, 86, 85, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 177, 177, 177, 138, 138, 86, 85, 26, 5, 1, 1, 1, 1, 86, 86] 177
rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 585
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037234 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 110, 111, 169, 177, 177, 169, 177, 177, 177, 30, 30, 1, 1, 1, 8, 8, 30, 30, 110, 168, 177, 177, 177, 177, 31, 30] 177
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])
total number of confs: 513
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037234 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037234
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037234/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037234
Building REAL300000037235
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037235'
/scratch/stefan/7769618/working/building/REAL300000037235 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037235

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037235/0 /scratch/stefan/7769618/working/building/REAL300000037235 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/245
`/scratch/stefan/7769618/working/3D/245' -> `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=C2Cl)=C1O)

`REAL300000037235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037235 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2Cl)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 19, 6, 1, 1, 1, 1, 70] 70
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 126
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037235 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2Cl)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 35, 35, 27, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 10, 27, 35, 35, 27, 35, 2] 70
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, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 109
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037235 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037235
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037235/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037235
Building REAL300000037236
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037236'
/scratch/stefan/7769618/working/building/REAL300000037236 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037236

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037236/0 /scratch/stefan/7769618/working/building/REAL300000037236 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/246
`/scratch/stefan/7769618/working/3D/246' -> `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=CC=C3Cl)C=C2)=C1)

`REAL300000037236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037236 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 30, 46, 46, 34, 46, 46, 46, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 6, 29, 46, 46, 38, 46, 1, 1, 3] 82
rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 40, 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, 38, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037236 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 50, 42, 42, 46, 46, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 50, 82, 82, 50, 50, 50, 46, 46, 21, 6, 1, 1, 1, 1, 46, 46, 50] 82
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])
total number of confs: 297
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037236 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 40, 50, 50, 43, 50, 50, 50, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 10, 39, 50, 50, 49, 50, 3, 3, 1] 82
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 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])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037236 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037236
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037236/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037236
Building REAL300000037237
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037237'
/scratch/stefan/7769618/working/building/REAL300000037237 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037237

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037237/0 /scratch/stefan/7769618/working/building/REAL300000037237 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/247
`/scratch/stefan/7769618/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000037237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037237 none CCOC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 19, 19, 19, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 88, 176, 182, 182, 91, 91, 91, 91, 91, 19, 6, 4, 1, 1, 1, 1, 19, 19, 176, 176] 201
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 768
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037237 none CCOC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 1, 1, 1, 1, 1, 7, 7, 15, 19, 19, 15, 19, 19, 19, 1, 1, 1, 1, 9, 41, 70, 70, 29, 29, 29, 29, 29, 1, 7, 15, 19, 19, 15, 19, 1, 1, 41, 41] 201
rigid atoms, others: [2, 3, 4, 5, 6, 16, 17, 18, 19, 36, 29, 37] 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, 38, 39])
total number of confs: 379
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037237 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037237
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037237/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037237
Building REAL300000037238
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037238'
/scratch/stefan/7769618/working/building/REAL300000037238 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037238

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037238/0 /scratch/stefan/7769618/working/building/REAL300000037238 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/248
`/scratch/stefan/7769618/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000037238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037238 none CC(N=NC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 39, 39, 47, 47, 43, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 47, 47, 47, 47, 1, 1, 1, 1] 47
rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037238 none CC(N=NC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 1, 1, 1, 1, 47, 47, 47, 47] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037238 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037238/1 /scratch/stefan/7769618/working/building/REAL300000037238 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/249
`/scratch/stefan/7769618/working/3D/249' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000037238.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037238/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037238 none CC(=NNC1=CC=CC=C1Cl)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', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 8, 8, 27, 35, 35, 27, 35, 35, 35, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 35, 35, 28, 35, 1, 1, 1, 1] 35
rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 109
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037238 none CC(=NNC1=CC=CC=C1Cl)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', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 6, 1, 1, 1, 1, 35, 35, 35, 35] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 58
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037238 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037238
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037238/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037238/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037238
Building REAL300000037239
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037239'
/scratch/stefan/7769618/working/building/REAL300000037239 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037239

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037239/0 /scratch/stefan/7769618/working/building/REAL300000037239 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/250
`/scratch/stefan/7769618/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3Cl)C2=CC=C1)

`REAL300000037239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037239 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 22, 22, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 22, 22, 9, 5, 1, 1, 1, 1, 23, 23, 23] 23
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
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: REAL300000037239 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 23, 23, 19, 23, 22, 22, 1, 1, 1, 1, 1, 1, 6, 18, 23, 23, 23, 23, 1, 1, 1] 23
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29])
total number of confs: 77
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037239 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037239
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037239/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037239
Building REAL300000037240
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037240'
/scratch/stefan/7769618/working/building/REAL300000037240 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037240

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037240/0 /scratch/stefan/7769618/working/building/REAL300000037240 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/251
`/scratch/stefan/7769618/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037240 none CC(=NNC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 18, 22, 22, 18, 22, 22, 22, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 22, 22, 22, 22, 1, 1, 1, 1, 1] 22
rigid atoms, others: [32, 1, 34, 35, 36, 33, 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])
total number of confs: 77
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037240 none CC(=NNC1=CC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 6, 1, 1, 1, 1, 22, 22, 22, 22, 22] 22
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36])
total number of confs: 37
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037240 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037240
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037240/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037240
Building REAL300000037241
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037241'
/scratch/stefan/7769618/working/building/REAL300000037241 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037241

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037241/0 /scratch/stefan/7769618/working/building/REAL300000037241 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/252
`/scratch/stefan/7769618/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3Cl)=CC=C2O1)

`REAL300000037241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037241 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 12, 6, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
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: REAL300000037241 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 16, 21, 21, 17, 21, 21, 21, 1, 1, 1, 1, 1, 1, 8, 16, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037241 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037241
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037241/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037241
Building REAL300000037242
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037242'
/scratch/stefan/7769618/working/building/REAL300000037242 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037242

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037242/0 /scratch/stefan/7769618/working/building/REAL300000037242 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/253
`/scratch/stefan/7769618/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3Cl)=CC=CN12)

`REAL300000037242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037242 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 12, 11, 5, 1, 1, 1, 1, 13, 13, 13] 13
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037242 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 8, 12, 12, 10, 12, 12, 13, 1, 1, 1, 1, 1, 4, 8, 13, 13, 11, 12, 1, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037242 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037242
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037242/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037242
Building REAL300000037243
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037243'
/scratch/stefan/7769618/working/building/REAL300000037243 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037243

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037243/0 /scratch/stefan/7769618/working/building/REAL300000037243 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/254
`/scratch/stefan/7769618/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2Cl)O1)

`REAL300000037243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037243 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [139, 139, 139, 139, 139, 139, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 16, 16, 9, 16, 16, 16, 139, 139, 139, 35, 35, 1, 1, 1, 1, 4, 9, 16, 16, 9, 16] 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])
total number of confs: 294
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037243 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 135, 50, 16, 16, 16, 16, 16, 16, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 135, 135, 16, 16, 16, 16, 10, 4, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 530
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037243 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 53, 139, 139, 139, 139, 139, 139, 185, 185, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 139, 139, 139, 139, 185, 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])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037243 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037243
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037243/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037243
Building REAL300000037244
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037244'
/scratch/stefan/7769618/working/building/REAL300000037244 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037244

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037244/0 /scratch/stefan/7769618/working/building/REAL300000037244 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/255
`/scratch/stefan/7769618/working/3D/255' -> `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=C2Cl)C=C1Cl)

`REAL300000037244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037244 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 162, 69, 37, 69, 68, 20, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 201, 201, 69, 68, 19, 3, 1, 1, 1, 1, 69] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32])
total number of confs: 565
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: REAL300000037244 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 42, 72, 9, 1, 1, 1, 1, 1, 1, 9, 9, 40, 68, 68, 41, 68, 68, 69, 1, 1, 1, 42, 42, 1, 1, 9, 40, 69, 69, 68, 68, 1] 201
rigid atoms, others: [32, 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])
total number of confs: 476
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037244 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037244
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037244/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037244
Building REAL300000037245
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037245'
/scratch/stefan/7769618/working/building/REAL300000037245 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037245

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037245/0 /scratch/stefan/7769618/working/building/REAL300000037245 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/256
`/scratch/stefan/7769618/working/3D/256' -> `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=C2Cl)C=C1)

`REAL300000037245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037245 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 31, 21, 13, 21, 21, 13, 21, 20, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 33, 33, 31, 21, 20, 9, 3, 1, 1, 1, 1, 21, 21] 33
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037245 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 14, 20, 20, 14, 20, 20, 20, 1, 1, 9, 9, 5, 1, 1, 6, 14, 20, 20, 14, 20, 1, 1] 33
rigid atoms, others: [35, 36, 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, 34])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037245 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037245
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037245/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037245
Building REAL300000037246
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037246'
/scratch/stefan/7769618/working/building/REAL300000037246 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037246

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037246/0 /scratch/stefan/7769618/working/building/REAL300000037246 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/257
`/scratch/stefan/7769618/working/3D/257' -> `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=C3Cl)C(F)=CC=C2S1)

`REAL300000037246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037246 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 18, 6, 1, 1, 1, 1, 29, 29] 29
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
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: REAL300000037246 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 22, 29, 29, 22, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 10, 22, 29, 29, 28, 29, 1, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 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/7769618/working/building/REAL300000037246 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037246
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037246/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037246
Building REAL300000037247
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037247'
/scratch/stefan/7769618/working/building/REAL300000037247 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037247

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037247/0 /scratch/stefan/7769618/working/building/REAL300000037247 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/258
`/scratch/stefan/7769618/working/3D/258' -> `0.mol2'
Preparing input files

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

`REAL300000037247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037247 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 19, 6, 1, 1, 1, 1] 26
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037247 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 26, 26, 21, 26, 26, 26, 3, 3, 3, 1, 1, 1, 9, 21, 26, 26, 23, 26] 26
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037247 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037247
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037247/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037247
Building REAL300000037248
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037248'
/scratch/stefan/7769618/working/building/REAL300000037248 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037248

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037248/0 /scratch/stefan/7769618/working/building/REAL300000037248 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/259
`/scratch/stefan/7769618/working/3D/259' -> `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=C3Cl)=N2)C1)

`REAL300000037248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 7, 7, 26, 44, 44, 26, 44, 44, 44, 1, 13, 13, 13, 1, 1, 7, 26, 44, 44, 27, 44, 13, 13] 128
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])
total number of confs: 201
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 128, 128, 128, 44, 128, 44, 44, 44, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 44, 128, 128, 128, 44, 44, 25, 6, 1, 1, 1, 1, 128, 128] 128
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 298
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 43, 43, 104, 128, 128, 104, 128, 128, 128, 13, 1, 1, 1, 13, 13, 43, 104, 128, 128, 106, 128, 1, 1] 128
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 373
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037248 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037248/1 /scratch/stefan/7769618/working/building/REAL300000037248 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/260
`/scratch/stefan/7769618/working/3D/260' -> `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=C3Cl)=N2)C1)

`REAL300000037248.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037248/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 19, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 9, 47, 47, 54, 54, 47, 54, 54, 54, 1, 10, 10, 10, 1, 1, 9, 9, 54, 54, 47, 54, 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, 35])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 54, 201, 54, 54, 54, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 54, 54, 15, 16, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 474
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037248 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 197, 197, 201, 201, 197, 201, 201, 201, 10, 1, 1, 1, 10, 10, 49, 49, 201, 201, 198, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037248 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037248
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037248/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037248/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037248
Building REAL300000037249
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037249'
/scratch/stefan/7769618/working/building/REAL300000037249 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037249

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037249/0 /scratch/stefan/7769618/working/building/REAL300000037249 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/261
`/scratch/stefan/7769618/working/3D/261' -> `0.mol2'
Preparing input files

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

`REAL300000037249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037249 none CON=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', '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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 82, 82, 19, 82, 9, 36, 36, 6, 1, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 36, 36, 85, 85, 85, 82, 82, 82, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 85
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41])
total number of confs: 283
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: REAL300000037249 none CON=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', '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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 52, 52, 36, 36, 1, 1, 22, 22, 22, 7, 7, 7, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1] 85
rigid atoms, others: [3, 5, 6, 7, 8, 9, 40, 21, 22, 41, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 162
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037249 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037249
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037249/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037249
Building REAL300000037250
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037250'
/scratch/stefan/7769618/working/building/REAL300000037250 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037250

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037250/0 /scratch/stefan/7769618/working/building/REAL300000037250 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/262
`/scratch/stefan/7769618/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=C(C)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1)

`REAL300000037250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037250 none CON=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', '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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 78, 87, 130, 137, 137, 1, 1, 15, 15, 15, 6, 6, 6, 1, 1, 27, 27, 27, 78, 78, 91, 90, 128, 128, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 20, 21, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 675
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037250 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037250
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037250/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037250
Building REAL300000037251
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037251'
/scratch/stefan/7769618/working/building/REAL300000037251 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037251

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037251/0 /scratch/stefan/7769618/working/building/REAL300000037251 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/263
`/scratch/stefan/7769618/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=C(C)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000037251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037251 none CON=C(C)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 121, 201, 105, 121, 121, 67, 22, 67, 67, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 121, 121, 22, 4, 4, 1, 1, 1, 1, 121, 121] 201
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 717
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: REAL300000037251 none CON=C(C)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 53, 121, 121, 53, 121, 121, 121, 121, 121, 1, 1, 21, 21, 21, 7, 7, 7, 1, 1, 9, 53, 53, 121, 121, 121, 121, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 40, 41, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 554
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037251 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037251
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037251/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037251
Building REAL300000037252
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037252'
/scratch/stefan/7769618/working/building/REAL300000037252 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037252

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037252/0 /scratch/stefan/7769618/working/building/REAL300000037252 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/264
`/scratch/stefan/7769618/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1)

`REAL300000037252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037252 none CON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
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, 5, 9, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 9
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41])
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: REAL300000037252 none CON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 9
rigid atoms, others: [3, 5, 6, 7, 8, 9, 40, 21, 22, 41, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 26
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037252 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037252
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037252/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037252
Building REAL300000037253
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037253'
/scratch/stefan/7769618/working/building/REAL300000037253 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037253

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037253/0 /scratch/stefan/7769618/working/building/REAL300000037253 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/265
`/scratch/stefan/7769618/working/3D/265' -> `0.mol2'
Preparing input files

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

`REAL300000037253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037253 none CON=C(C)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 55, 102, 132, 126, 1, 1, 27, 27, 27, 7, 7, 7, 1, 1, 9, 55, 55, 102, 102, 1, 1] 201
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 589
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037253 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037253
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037253/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037253
Building REAL300000037254
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037254'
/scratch/stefan/7769618/working/building/REAL300000037254 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037254

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037254/0 /scratch/stefan/7769618/working/building/REAL300000037254 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/266
`/scratch/stefan/7769618/working/3D/266' -> `0.mol2'
Preparing input files

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

`REAL300000037254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037254 none CON=C(C)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 51, 72, 114, 123, 123, 1, 1, 18, 18, 18, 6, 6, 6, 1, 1, 9, 51, 51, 80, 80, 108, 108, 1, 1] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 19, 20, 27, 28, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 597
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037254 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037254
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037254/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037254
Building REAL300000037255
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037255'
/scratch/stefan/7769618/working/building/REAL300000037255 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037255

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037255/0 /scratch/stefan/7769618/working/building/REAL300000037255 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/267
`/scratch/stefan/7769618/working/3D/267' -> `0.mol2'
Preparing input files

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

`REAL300000037255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037255 none CON=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', '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']
dock atom type numbers: [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, 6, 7, 7, 7, 7, 7]
dock color type numbers: [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]
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: [18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 26, 39, 39, 1, 1, 18, 18, 18, 7, 7, 7, 1, 1, 9, 26, 26, 26, 1, 1] 76
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 19, 20, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 182
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037255 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037255
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037255/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037255
Building REAL300000037256
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037256'
/scratch/stefan/7769618/working/building/REAL300000037256 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037256

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037256/0 /scratch/stefan/7769618/working/building/REAL300000037256 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/268
`/scratch/stefan/7769618/working/3D/268' -> `0.mol2'
Preparing input files

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

`REAL300000037256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037256 none CON=C(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 13, 31, 13, 13, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 31, 31, 31, 31, 31, 31, 13, 13, 4, 1, 1, 1, 1, 13, 13] 31
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037256 none CON=C(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 9, 11, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 13, 13, 13, 13, 1, 1] 31
rigid atoms, others: [3, 5, 6, 7, 8, 9, 22, 23, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037256 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037256/1 /scratch/stefan/7769618/working/building/REAL300000037256 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/269
`/scratch/stefan/7769618/working/3D/269' -> `1.mol2'
Preparing input files

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

`REAL300000037256.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037256/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037256 none CON=C(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 29, 9, 13, 13, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 29, 29, 29, 13, 13, 1, 1, 1, 1, 13, 13] 29
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
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: REAL300000037256 none CON=C(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 9, 11, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 13, 13, 13, 13, 1, 1] 29
rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 22, 23, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037256 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037256
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037256/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037256/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037256
Building REAL300000037257
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037257'
/scratch/stefan/7769618/working/building/REAL300000037257 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037257

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037257/0 /scratch/stefan/7769618/working/building/REAL300000037257 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/270
`/scratch/stefan/7769618/working/3D/270' -> `0.mol2'
Preparing input files

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

`REAL300000037257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037257 none CON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 114, 112, 152, 152, 88, 18, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 152, 152, 152, 201, 201, 201, 201, 152, 152, 18, 18, 9, 9, 1, 152] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33])
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: REAL300000037257 none CON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 6, 1, 1, 1, 1, 1, 1, 10, 31, 41, 152, 152, 152, 152, 152, 152, 152, 1, 1, 1, 18, 18, 18, 6, 1, 1, 31, 31, 41, 41, 152, 1] 201
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 19, 20, 21, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037257 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037257
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037257/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037257
Building REAL300000037258
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037258'
/scratch/stefan/7769618/working/building/REAL300000037258 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037258

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037258/0 /scratch/stefan/7769618/working/building/REAL300000037258 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/271
`/scratch/stefan/7769618/working/3D/271' -> `0.mol2'
Preparing input files

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

`REAL300000037258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037258 none CON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 92, 201, 58, 18, 18, 36, 36, 18, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 201, 201, 201, 201, 201, 201, 92, 92, 58, 58, 36, 36, 8, 8, 1, 1, 1, 1, 36, 36] 201
rigid atoms, others: [38, 39, 40, 41, 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, 42, 43])
total number of confs: 807
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: REAL300000037258 none CON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 17, 17, 6, 17, 4, 1, 1, 1, 1, 1, 1, 2, 10, 36, 36, 36, 36, 36, 37, 37, 36, 1, 1, 21, 21, 21, 17, 17, 17, 6, 6, 4, 4, 1, 1, 10, 10, 36, 36, 36, 36, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 43, 22, 23, 42] 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, 36, 37, 38, 39, 40, 41])
total number of confs: 126
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037258 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037258
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037258/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037258
Building REAL300000037259
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037259'
/scratch/stefan/7769618/working/building/REAL300000037259 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037259

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037259/0 /scratch/stefan/7769618/working/building/REAL300000037259 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/272
`/scratch/stefan/7769618/working/3D/272' -> `0.mol2'
Preparing input files

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

`REAL300000037259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037259 none CON=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
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: [45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 65, 65, 45, 45, 45, 11, 11, 11, 1, 1, 1, 43, 43] 117
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27])
total number of confs: 282
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037259 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037259
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037259/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037259
Building REAL300000037260
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037260'
/scratch/stefan/7769618/working/building/REAL300000037260 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037260

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037260/0 /scratch/stefan/7769618/working/building/REAL300000037260 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/273
`/scratch/stefan/7769618/working/3D/273' -> `0.mol2'
Preparing input files

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

`REAL300000037260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037260 none CON=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [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]
dock color type numbers: [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]
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: [12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 3, 19, 27, 27, 12, 12, 12, 4, 1, 1, 4, 4, 4, 19, 19] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23] set([0, 1, 2, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037260 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037260
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037260/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037260
Building REAL300000037261
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037261'
/scratch/stefan/7769618/working/building/REAL300000037261 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037261

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037261/0 /scratch/stefan/7769618/working/building/REAL300000037261 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/274
`/scratch/stefan/7769618/working/3D/274' -> `0.mol2'
Preparing input files

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

`REAL300000037261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037261 none CON=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['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']
dock atom type numbers: [5, 12, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1] 7
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20] set([0, 1, 2, 14, 15, 16, 17])
total number of confs: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037261 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037261
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037261/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037261
Building REAL300000037262
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037262'
/scratch/stefan/7769618/working/building/REAL300000037262 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037262

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037262/0 /scratch/stefan/7769618/working/building/REAL300000037262 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/275
`/scratch/stefan/7769618/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1OCC(=O)[O-])

`REAL300000037262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037262 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [54, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 113, 197, 201, 201, 54, 54, 54, 27, 8, 1, 1, 1, 27, 27, 197, 197] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 592
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037262 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 46, 71, 71, 4, 4, 4, 1, 7, 27, 27, 27, 1, 1, 46, 46] 201
rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 16, 17, 25, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037262 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037262
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037262/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037262
Building REAL300000037263
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037263'
/scratch/stefan/7769618/working/building/REAL300000037263 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037263

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037263/0 /scratch/stefan/7769618/working/building/REAL300000037263 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/276
`/scratch/stefan/7769618/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NN1CC(=O)NC1=O)

`REAL300000037263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037263 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1CC(=O)NC1=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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 59, 20, 20, 20, 10, 20, 20, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 20, 20, 20, 10, 1, 1, 1] 88
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])
total number of confs: 273
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: REAL300000037263 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1CC(=O)NC1=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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 7, 7, 6, 4, 7, 6, 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: [60, 41, 60, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 41, 41, 1, 1, 1, 4, 20, 20, 20] 88
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29])
total number of confs: 223
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037263 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037263
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037263/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037263
Building REAL300000037264
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037264'
/scratch/stefan/7769618/working/building/REAL300000037264 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037264

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037264/0 /scratch/stefan/7769618/working/building/REAL300000037264 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/277
`/scratch/stefan/7769618/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1)

`REAL300000037264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037264 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 3, 3, 1, 8, 25, 25, 25, 1, 1, 1] 61
rigid atoms, others: [32, 37, 38, 39, 10, 11, 12, 13, 14, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037264 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 33, 33, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 61, 61, 61, 61, 33, 33, 25, 6, 1, 1, 1, 25, 25, 25] 61
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, 39])
total number of confs: 86
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037264 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 24, 24, 61, 61, 61, 61, 61, 61, 10, 11, 11, 1, 1, 1, 1, 5, 5, 11, 24, 61, 61, 61, 10, 11, 11] 61
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037264 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037264
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037264/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037264
Building REAL300000037265
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037265'
/scratch/stefan/7769618/working/building/REAL300000037265 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037265

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037265/0 /scratch/stefan/7769618/working/building/REAL300000037265 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/278
`/scratch/stefan/7769618/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=O)C=C1[N+](=O)[O-])

`REAL300000037265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037265 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 8, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 3, 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, 95, 21, 19, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 187, 187, 45, 45, 11, 1, 1, 1, 45] 187
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 630
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: REAL300000037265 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 8, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 3, 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: [49, 35, 49, 7, 1, 1, 1, 1, 1, 1, 12, 12, 45, 45, 45, 45, 45, 45, 1, 1, 1, 2, 2, 35, 35, 1, 1, 12, 45, 45, 45, 1] 187
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 239
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037265 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037265
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037265/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037265
Building REAL300000037266
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037266'
/scratch/stefan/7769618/working/building/REAL300000037266 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037266

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037266/0 /scratch/stefan/7769618/working/building/REAL300000037266 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/279
`/scratch/stefan/7769618/working/3D/279' -> `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=NN3CC(=O)NC3=O)C=C2)=C1)

`REAL300000037266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037266 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3CC(=O)NC3=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 36, 43, 43, 36, 12, 2, 1, 1, 1, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 20, 1, 1, 36, 36, 36, 36, 12, 12, 1, 1, 11, 20, 20, 20, 1, 1, 36] 201
rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 135
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037266 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3CC(=O)NC3=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 61, 24, 15, 13, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 61, 61, 20, 20, 7, 1, 1, 1, 20, 20, 201] 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, 39])
total number of confs: 392
number of broken/clashed sets: 85
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037266 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3CC(=O)NC3=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 30, 36, 36, 30, 30, 111, 111, 201, 201, 201, 201, 201, 201, 36, 36, 1, 2, 2, 2, 9, 9, 36, 36, 111, 201, 201, 201, 35, 36, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 39, 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])
total number of confs: 448
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037266 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037266
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037266/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037266
Building REAL300000037267
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037267'
/scratch/stefan/7769618/working/building/REAL300000037267 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037267

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037267/0 /scratch/stefan/7769618/working/building/REAL300000037267 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/280
`/scratch/stefan/7769618/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(COC2=CC(C=NN3CC(=O)NC3=O)=CC=C2)=CC=C1)

`REAL300000037267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037267 none O=C([O-])C1=CC(COC2=CC(C=NN3CC(=O)NC3=O)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 35, 35, 8, 3, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 1, 1, 1, 35, 35, 35, 36, 8, 8, 1, 8, 19, 19, 19, 1, 1, 1, 36, 36, 35] 201
rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 20, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 100
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037267 none O=C([O-])C1=CC(COC2=CC(C=NN3CC(=O)NC3=O)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 49, 33, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 201, 201, 201, 201, 49, 49, 19, 6, 1, 1, 1, 19, 19, 19, 201, 201, 201] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39])
total number of confs: 311
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037267 none O=C([O-])C1=CC(COC2=CC(C=NN3CC(=O)NC3=O)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 25, 35, 35, 36, 121, 121, 201, 201, 201, 201, 201, 201, 35, 35, 35, 1, 1, 1, 1, 8, 8, 36, 121, 201, 201, 201, 35, 35, 35, 1, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 39, 23, 24, 25, 26, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 404
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037267 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037267
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037267/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037267
Building REAL300000037268
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037268'
/scratch/stefan/7769618/working/building/REAL300000037268 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037268

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037268/0 /scratch/stefan/7769618/working/building/REAL300000037268 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/281
`/scratch/stefan/7769618/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NN3CC(=O)NC3=O)C=C2)OC=C1)

`REAL300000037268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037268 none O=C([O-])C1=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 1, 1, 7, 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, 7, 6, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 12, 9, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 1, 1, 9, 9, 9, 5, 5, 1, 1, 8, 25, 25, 25, 1, 1, 9, 9] 56
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36])
total number of confs: 72
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037268 none O=C([O-])C1=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 1, 1, 7, 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, 7, 6, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 37, 25, 14, 13, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 56, 56, 56, 37, 37, 25, 25, 8, 1, 1, 1, 25, 25, 56, 56] 56
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 160
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037268 none O=C([O-])C1=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 1, 1, 7, 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, 7, 6, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 29, 29, 56, 56, 56, 56, 56, 56, 9, 9, 1, 1, 1, 5, 5, 9, 9, 29, 56, 56, 56, 9, 9, 1, 1] 56
rigid atoms, others: [1, 3, 4, 5, 35, 22, 23, 24, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 131
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037268 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037268
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037268/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037268
Building REAL300000037269
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037269'
/scratch/stefan/7769618/working/building/REAL300000037269 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037269

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037269/0 /scratch/stefan/7769618/working/building/REAL300000037269 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/282
`/scratch/stefan/7769618/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NN2CC(=O)NC2=O)C(OCC(=O)[O-])=C1)

`REAL300000037269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037269 none COC1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [36, 23, 12, 23, 23, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 69, 116, 121, 121, 23, 36, 36, 36, 23, 23, 12, 1, 1, 1, 116, 116, 23] 121
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 395
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: REAL300000037269 none COC1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 23, 23, 23, 23, 23, 23, 1, 1, 9, 44, 70, 70, 1, 3, 3, 3, 1, 1, 4, 23, 23, 23, 44, 44, 1] 121
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 15, 16, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 273
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037269 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037269
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037269/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037269
Building REAL300000037270
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037270'
/scratch/stefan/7769618/working/building/REAL300000037270 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037270

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037270/0 /scratch/stefan/7769618/working/building/REAL300000037270 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/283
`/scratch/stefan/7769618/working/3D/283' -> `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=NN2CC(=O)NC2=O)C=C1)

`REAL300000037270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037270 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 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, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 201, 44, 20, 44, 44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 11, 1, 1, 1, 44, 44] 201
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, 29])
total number of confs: 641
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037270 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 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, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 44, 7, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 10, 44, 44, 44, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037270 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037270
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037270/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037270
Building REAL300000037271
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037271'
/scratch/stefan/7769618/working/building/REAL300000037271 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037271

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037271/0 /scratch/stefan/7769618/working/building/REAL300000037271 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/284
`/scratch/stefan/7769618/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NN1CC(=O)NC1=O)

`REAL300000037271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037271 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1CC(=O)NC1=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 6, 4, 7, 6, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 6, 1, 1, 1] 12
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])
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: REAL300000037271 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1CC(=O)NC1=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 6, 4, 7, 6, 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, 9, 9, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 9, 12, 12, 12] 12
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 22] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 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/7769618/working/building/REAL300000037271 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037271
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037271/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037271
Building REAL300000037272
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037272'
/scratch/stefan/7769618/working/building/REAL300000037272 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037272

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037272/0 /scratch/stefan/7769618/working/building/REAL300000037272 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/285
`/scratch/stefan/7769618/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=O)C=C1Br)

`REAL300000037272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037272 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 17, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 15, 15, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 201, 201, 44, 44, 8, 1, 1, 1, 44] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 641
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: REAL300000037272 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 17, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 68, 8, 1, 1, 1, 1, 1, 1, 10, 10, 44, 44, 44, 44, 44, 44, 1, 1, 1, 41, 41, 1, 1, 10, 44, 44, 44, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28])
total number of confs: 289
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037272 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037272
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037272/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037272
Building REAL300000037273
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037273'
/scratch/stefan/7769618/working/building/REAL300000037273 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037273

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037273/0 /scratch/stefan/7769618/working/building/REAL300000037273 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/286
`/scratch/stefan/7769618/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2CC(=O)NC2=O)C=C1)

`REAL300000037273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037273 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 19, 19] 19
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 31, 32])
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: REAL300000037273 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 19, 19, 19, 19, 19, 19, 1, 1, 3, 3, 3, 1, 10, 19, 19, 19, 1, 1] 19
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 21, 22, 26, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037273 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037273
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037273/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037273
Building REAL300000037274
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037274'
/scratch/stefan/7769618/working/building/REAL300000037274 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037274

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037274/0 /scratch/stefan/7769618/working/building/REAL300000037274 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/287
`/scratch/stefan/7769618/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(C=NN3CC(=O)NC3=O)C=C2Cl)N=N1)

`REAL300000037274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037274 none O=C([O-])C1=CN(CCOC2=CC=C(C=NN3CC(=O)NC3=O)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 33, 29, 9, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 1, 1, 1, 75, 75, 75, 33, 33, 29, 29, 1, 1, 6, 15, 15, 15, 1] 201
rigid atoms, others: [32, 33, 38, 8, 9, 10, 11, 12, 13, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037274 none O=C([O-])C1=CN(CCOC2=CC=C(C=NN3CC(=O)NC3=O)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 124, 118, 52, 15, 7, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 201, 201, 201, 123, 123, 119, 119, 16, 16, 4, 1, 1, 1, 15] 201
rigid atoms, others: [35, 36, 37, 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, 38])
total number of confs: 555
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037274 none O=C([O-])C1=CN(CCOC2=CC=C(C=NN3CC(=O)NC3=O)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 15, 41, 75, 75, 49, 75, 109, 109, 201, 201, 201, 201, 201, 201, 75, 75, 75, 1, 1, 1, 8, 8, 15, 15, 75, 75, 109, 201, 201, 201, 75] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 547
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037274 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037274
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037274/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037274
Building REAL300000037275
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037275'
/scratch/stefan/7769618/working/building/REAL300000037275 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037275

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037275/0 /scratch/stefan/7769618/working/building/REAL300000037275 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/288
`/scratch/stefan/7769618/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2CC(=O)NC2=O)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000037275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037275 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 119, 200, 201, 201, 64, 64, 64, 29, 10, 1, 1, 1, 29, 200, 200] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 589
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: REAL300000037275 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 1, 1, 1, 9, 46, 73, 73, 4, 4, 4, 1, 7, 29, 29, 29, 1, 46, 46] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 14, 15, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35])
total number of confs: 295
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037275 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037275
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037275/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037275
Building REAL300000037276
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037276'
/scratch/stefan/7769618/working/building/REAL300000037276 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037276

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037276/0 /scratch/stefan/7769618/working/building/REAL300000037276 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/289
`/scratch/stefan/7769618/working/3D/289' -> `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=NN1CC(=O)NC1=O)

`REAL300000037276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037276 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1] 4
rigid atoms, others: [34, 35, 36, 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])
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: REAL300000037276 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 1, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 1, 1, 1, 3, 4, 4, 4] 4
rigid atoms, others: [32, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037276 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037276
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037276/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037276
Building REAL300000037277
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037277'
/scratch/stefan/7769618/working/building/REAL300000037277 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037277

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037277/0 /scratch/stefan/7769618/working/building/REAL300000037277 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/290
`/scratch/stefan/7769618/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2CC(=O)NC2=O)=CC=C1OCCC(=O)[O-])

`REAL300000037277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037277 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 98, 178, 195, 201, 198, 59, 59, 59, 32, 8, 1, 1, 1, 32, 32, 178, 178, 195, 195] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 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: REAL300000037277 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 9, 37, 50, 77, 71, 3, 3, 3, 1, 7, 32, 32, 32, 1, 1, 37, 37, 49, 49] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 14, 15, 16, 17, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037277 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037277
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037277/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037277
Building REAL300000037278
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037278'
/scratch/stefan/7769618/working/building/REAL300000037278 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037278

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037278/0 /scratch/stefan/7769618/working/building/REAL300000037278 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/291
`/scratch/stefan/7769618/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NN2CC(=O)NC2=O)C2=CC=CC=C21)

`REAL300000037278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037278 none O=C([O-])CN1C=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 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, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 71, 71, 29, 8, 1, 1, 1, 29, 29, 29, 29] 71
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
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: REAL300000037278 none O=C([O-])CN1C=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 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, 6, 4, 7, 6, 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: [14, 8, 14, 1, 1, 1, 1, 1, 10, 10, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 29, 29, 29, 1, 1, 1, 1] 71
rigid atoms, others: [32, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 24, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037278 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037278
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037278/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037278
Building REAL300000037279
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037279'
/scratch/stefan/7769618/working/building/REAL300000037279 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037279

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037279/0 /scratch/stefan/7769618/working/building/REAL300000037279 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/292
`/scratch/stefan/7769618/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC(C=NN2CC(=O)NC2=O)=CC=C1)C1=CC=CC=C1)

`REAL300000037279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037279 none O=C([O-])C(OC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 201, 92, 20, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 198, 201, 201, 198, 201, 201, 198, 20, 7, 1, 1, 1, 19, 19, 19, 201, 201, 198, 201, 201] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 637
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037279 none O=C([O-])C(OC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 3, 9, 43, 43, 43, 104, 104, 201, 201, 201, 201, 201, 201, 43, 43, 43, 1, 1, 1, 1, 1, 1, 3, 43, 104, 201, 201, 201, 43, 43, 43, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 36, 37, 38, 39, 35, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 409
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037279 none O=C([O-])C(OC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 31, 38, 11, 1, 1, 1, 1, 1, 4, 4, 19, 19, 19, 19, 19, 19, 1, 1, 1, 31, 43, 43, 31, 43, 43, 31, 1, 4, 19, 19, 19, 1, 1, 1, 43, 43, 31, 43, 43] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 17, 18, 19, 27] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 214
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037279 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037279
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037279/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037279
Building REAL300000037280
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037280'
/scratch/stefan/7769618/working/building/REAL300000037280 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037280

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037280/0 /scratch/stefan/7769618/working/building/REAL300000037280 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/293
`/scratch/stefan/7769618/working/3D/293' -> `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=NN3CC(=O)NC3=O)C=C2)C=C1)

`REAL300000037280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037280 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 3, 3, 3, 3, 1, 1, 6, 11, 11, 11, 1, 1, 3, 3] 11
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35])
total number of confs: 34
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037280 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 8, 11, 9, 11, 11, 8, 8, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 11, 11, 11, 10, 10, 8, 1, 1, 1, 10, 10, 11, 11] 11
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 44
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037280 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 11, 11, 3, 3, 1, 1] 11
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 32
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037280 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037280
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037280/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037280
Building REAL300000037281
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037281'
/scratch/stefan/7769618/working/building/REAL300000037281 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037281

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037281/0 /scratch/stefan/7769618/working/building/REAL300000037281 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/294
`/scratch/stefan/7769618/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2CC(=O)NC2=O)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037281 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 6, 4, 7, 6, 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
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [89, 43, 43, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 43, 43, 43, 110, 167, 167, 183, 183, 89, 89, 89, 43, 9, 1, 1, 1, 43, 167, 167, 167, 167] 183
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 590
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: REAL300000037281 none COC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 6, 4, 7, 6, 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
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 6, 15, 15, 24, 24, 3, 3, 3, 1, 12, 43, 43, 43, 1, 15, 15, 15, 15] 183
rigid atoms, others: [32, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 149
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037281 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037281
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037281/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037281
Building REAL300000037282
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037282'
/scratch/stefan/7769618/working/building/REAL300000037282 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037282

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037282/0 /scratch/stefan/7769618/working/building/REAL300000037282 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/295
`/scratch/stefan/7769618/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=O)O2)=CC=C1O)

`REAL300000037282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037282 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 38, 38, 38, 1, 13, 13, 12, 12, 13, 1, 1, 10, 38, 38, 38, 13, 13, 26] 224
rigid atoms, others: [5, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037282 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 112, 112, 38, 38, 38, 38, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 38, 112, 112, 112, 112, 112, 38, 38, 10, 1, 1, 1, 112, 112, 224] 224
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, 32, 33])
total number of confs: 363
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037282 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 61, 61, 112, 112, 112, 112, 112, 112, 13, 1, 1, 1, 1, 1, 13, 13, 61, 112, 112, 112, 1, 1, 2] 224
rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037282 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037282
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037282/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037282
Building REAL300000037283
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037283'
/scratch/stefan/7769618/working/building/REAL300000037283 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037283

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037283/0 /scratch/stefan/7769618/working/building/REAL300000037283 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/296
`/scratch/stefan/7769618/working/3D/296' -> `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=NN3CC(=O)NC3=O)S2)C=C1)

`REAL300000037283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037283 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [6, 1, 6, 1, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 1, 5, 5, 5, 5, 1, 1, 10, 25, 25, 25, 5, 5] 35
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037283 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 25, 35, 25, 35, 35, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 35, 25, 25, 8, 1, 1, 1, 35, 35] 35
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 103
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037283 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 21, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 6, 6, 21, 35, 35, 35, 1, 1] 35
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037283 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037283
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037283/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037283
Building REAL300000037284
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037284'
/scratch/stefan/7769618/working/building/REAL300000037284 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037284

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037284/0 /scratch/stefan/7769618/working/building/REAL300000037284 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/297
`/scratch/stefan/7769618/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=O)S2)=CC=C1)

`REAL300000037284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037284 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=O)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 1, 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, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 1, 12, 12, 11, 12, 1, 1, 10, 24, 24, 24, 12, 12, 11] 64
rigid atoms, others: [5, 6, 7, 8, 9, 10, 19, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037284 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=O)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 1, 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, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 24, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 24, 64, 64, 64, 64, 24, 24, 8, 1, 1, 1, 64, 64, 64] 64
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 86
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037284 none O=C([O-])C1=CC(C2=CC=C(C=NN3CC(=O)NC3=O)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 1, 1, 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, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 12, 12, 12, 44, 44, 64, 64, 64, 64, 64, 64, 12, 1, 1, 1, 1, 12, 12, 44, 64, 64, 64, 1, 1, 1] 64
rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037284 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037284
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037284/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037284
Building REAL300000037285
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037285'
/scratch/stefan/7769618/working/building/REAL300000037285 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037285

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037285/0 /scratch/stefan/7769618/working/building/REAL300000037285 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/298
`/scratch/stefan/7769618/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NN3CC(=O)NC3=O)C2=C1)

`REAL300000037285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037285 none O=C([O-])C1=CC=C2SC=C(C=NN3CC(=O)NC3=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 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, 6, 4, 7, 6, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 11] 11
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 28])
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: REAL300000037285 none O=C([O-])C1=CC=C2SC=C(C=NN3CC(=O)NC3=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 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, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 11, 1] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037285 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037285
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037285/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037285
Building REAL300000037286
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037286'
/scratch/stefan/7769618/working/building/REAL300000037286 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037286

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037286/0 /scratch/stefan/7769618/working/building/REAL300000037286 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/299
`/scratch/stefan/7769618/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NN2CC(=O)NC2=O)=C1)

`REAL300000037286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037286 none O=C([O-])C1=CC=C(Br)C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 4, 7, 6, 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 6, 1, 1, 1, 14] 14
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 25])
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: REAL300000037286 none O=C([O-])C1=CC=C(Br)C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037286 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037286
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037286/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037286
Building REAL300000037287
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037287'
/scratch/stefan/7769618/working/building/REAL300000037287 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037287

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037287/0 /scratch/stefan/7769618/working/building/REAL300000037287 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/300
`/scratch/stefan/7769618/working/3D/300' -> `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=NN2CC(=O)NC2=O)=C1)

`REAL300000037287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037287 none O=C([O-])C1=CC(Br)=C(O)C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 1, 11, 1, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 6, 1, 1, 1, 11] 22
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 26])
total number of confs: 37
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: REAL300000037287 none O=C([O-])C1=CC(Br)=C(O)C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 1, 11, 1, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 2, 6, 11, 11, 11, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 23
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037287 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037287/1 /scratch/stefan/7769618/working/building/REAL300000037287 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/301
`/scratch/stefan/7769618/working/3D/301' -> `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=NN2CC(=O)NC2=O)=C1)

`REAL300000037287.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037287/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037287 none O=C([O-])C1=CC(Br)=C([O-])C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 8, 8, 6, 1, 1, 1, 8] 8
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 25])
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: REAL300000037287 none O=C([O-])C1=CC(Br)=C([O-])C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 6, 6, 8, 8, 8, 8, 8, 8, 1, 1, 6, 8, 8, 8, 1] 8
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24])
total number of confs: 16
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037287 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037287
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037287/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037287/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037287
Building REAL300000037288
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037288'
/scratch/stefan/7769618/working/building/REAL300000037288 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037288

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037288/0 /scratch/stefan/7769618/working/building/REAL300000037288 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/302
`/scratch/stefan/7769618/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(C=NN2CC(=O)NC2=O)=C1OCC(=O)[O-])

`REAL300000037288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037288 none COC1=CC(Br)=CC(C=NN2CC(=O)NC2=O)=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 17, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
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: REAL300000037288 none COC1=CC(Br)=CC(C=NN2CC(=O)NC2=O)=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 17, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3] 3
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])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037288 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037288
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037288/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037288
Building REAL300000037289
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037289'
/scratch/stefan/7769618/working/building/REAL300000037289 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037289

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037289/0 /scratch/stefan/7769618/working/building/REAL300000037289 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/303
`/scratch/stefan/7769618/working/3D/303' -> `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=NN3CC(=O)NC3=O)C=C2)O1)

`REAL300000037289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037289 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 3, 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: [33, 32, 33, 32, 32, 32, 11, 2, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 36, 36, 1, 1, 32, 32, 32, 11, 11, 1, 1, 11, 36, 36, 36, 1, 1] 137
rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 124
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037289 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 3, 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, 82, 42, 17, 17, 36, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 137, 137, 137, 82, 82, 36, 36, 10, 1, 1, 1, 36, 36] 137
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 385
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037289 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 26, 32, 32, 26, 26, 72, 72, 137, 137, 137, 137, 137, 137, 32, 32, 1, 1, 1, 8, 8, 32, 32, 72, 137, 137, 137, 32, 32] 137
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 322
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037289 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037289
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037289/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037289
Building REAL300000037290
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037290'
/scratch/stefan/7769618/working/building/REAL300000037290 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037290

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037290/0 /scratch/stefan/7769618/working/building/REAL300000037290 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/304
`/scratch/stefan/7769618/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NN2CC(=O)NC2=O)=CC(I)=C1)

`REAL300000037290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037290 none O=C([O-])C1=CC(C=NN2CC(=O)NC2=O)=CC(I)=C1 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 18, 1, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 6, 1, 1, 1, 13, 13] 13
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, 25])
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: REAL300000037290 none O=C([O-])C1=CC(C=NN2CC(=O)NC2=O)=CC(I)=C1 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 18, 1, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 9, 9, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 13, 13, 1, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037290 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037290
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037290/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037290
Building REAL300000037291
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037291'
/scratch/stefan/7769618/working/building/REAL300000037291 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037291

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037291/0 /scratch/stefan/7769618/working/building/REAL300000037291 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/305
`/scratch/stefan/7769618/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NN2CC(=O)NC2=O)=C1O)

`REAL300000037291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037291 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 7, 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, 7, 6, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 48] 48
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32])
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: REAL300000037291 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 12, 7, 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, 7, 6, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 2] 48
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037291 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037291
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037291/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037291
Building REAL300000037292
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037292'
/scratch/stefan/7769618/working/building/REAL300000037292 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037292

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037292/0 /scratch/stefan/7769618/working/building/REAL300000037292 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/306
`/scratch/stefan/7769618/working/3D/306' -> `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=NN3CC(=O)NC3=O)C=C2)=C1)

`REAL300000037292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037292 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [11, 5, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 17, 17, 17, 1, 1, 3] 47
rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037292 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 25, 25, 23, 25, 25, 17, 15, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 25, 47, 47, 25, 25, 25, 17, 17, 6, 1, 1, 1, 17, 17, 25] 47
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, 36, 37, 38])
total number of confs: 187
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037292 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3CC(=O)NC3=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 17, 25, 25, 25, 25, 25, 25, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 25, 25, 25, 3, 3, 1] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 38, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037292 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037292
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037292/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037292
Building REAL300000037293
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037293'
/scratch/stefan/7769618/working/building/REAL300000037293 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037293

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037293/0 /scratch/stefan/7769618/working/building/REAL300000037293 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/307
`/scratch/stefan/7769618/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NN2CC(=O)NC2=O)=CC=C1OCC(=O)[O-])

`REAL300000037293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037293 none CCOC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [81, 49, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 80, 170, 184, 184, 81, 81, 81, 81, 81, 17, 4, 1, 1, 1, 17, 17, 170, 170] 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])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037293 none CCOC1=CC(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [25, 9, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 9, 36, 50, 50, 25, 25, 25, 25, 25, 1, 7, 17, 17, 17, 1, 1, 36, 36] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 34, 15, 16, 17, 18, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 35, 36])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037293 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037293
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037293/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037293
Building REAL300000037294
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037294'
/scratch/stefan/7769618/working/building/REAL300000037294 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037294

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037294/0 /scratch/stefan/7769618/working/building/REAL300000037294 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/308
`/scratch/stefan/7769618/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1CC(=O)NC1=O)

`REAL300000037294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037294 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 24, 24, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 24, 38, 38, 38] 38
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 35, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 34])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037294 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [10, 9, 10, 9, 9, 9, 9, 38, 38, 38, 38, 38, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 6, 1, 1, 1] 38
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])
total number of confs: 87
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037294 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 2, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 4, 9, 9, 9] 38
rigid atoms, others: [32, 1, 3, 4, 5, 6, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037294 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037294
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037294/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037294
Building REAL300000037295
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037295'
/scratch/stefan/7769618/working/building/REAL300000037295 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037295

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037295/0 /scratch/stefan/7769618/working/building/REAL300000037295 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/309
`/scratch/stefan/7769618/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NN2CC(=O)NC2=O)=C1C(=O)[O-])

`REAL300000037295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037295 none CN1C2=CC=C(F)C=C2C(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 2, 2, 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1] 8
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])
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: REAL300000037295 none CN1C2=CC=C(F)C=C2C(C=NN2CC(=O)NC2=O)=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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 2, 2, 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, 8, 8, 8, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 8, 8] 8
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 28
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037295 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037295
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037295/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037295
Building REAL300000037296
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037296'
/scratch/stefan/7769618/working/building/REAL300000037296 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037296

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037296/0 /scratch/stefan/7769618/working/building/REAL300000037296 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/310
`/scratch/stefan/7769618/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NN2CC(=O)NC2=O)SC(Br)=C1)

`REAL300000037296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037296 none O=C([O-])C1=C(C=NN2CC(=O)NC2=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 17, 1, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 6, 1, 1, 1, 11] 11
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 22])
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: REAL300000037296 none O=C([O-])C1=C(C=NN2CC(=O)NC2=O)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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 14, 1, 17, 1, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 3, 11, 11, 11, 1] 11
rigid atoms, others: [1, 3, 4, 5, 14, 15, 16, 17, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21])
total number of confs: 24
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037296 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037296
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037296/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037296
Building REAL300000037297
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037297'
/scratch/stefan/7769618/working/building/REAL300000037297 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037297

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037297/0 /scratch/stefan/7769618/working/building/REAL300000037297 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/311
`/scratch/stefan/7769618/working/3D/311' -> `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=NN2CC(=O)NC2=O)O1)

`REAL300000037297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037297 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [111, 110, 111, 110, 110, 110, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 16, 110, 110, 110, 31, 31, 1, 1, 1, 1, 4, 16, 16, 16] 201
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 229
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037297 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 134, 50, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 134, 134, 16, 16, 16, 16, 8, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 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])
total number of confs: 538
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037297 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 48, 110, 110, 110, 110, 110, 110, 145, 145, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 110, 110, 110, 110, 145, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037297 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037297
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037297/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037297
Building REAL300000037298
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037298'
/scratch/stefan/7769618/working/building/REAL300000037298 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037298

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037298/0 /scratch/stefan/7769618/working/building/REAL300000037298 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/312
`/scratch/stefan/7769618/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NN1CC(=O)NC1=O)

`REAL300000037298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037298 none O=C([O-])C1=C(Br)C=CC=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 6, 4, 7, 6, 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, 6, 6, 6, 6, 1, 1, 1] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22])
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: REAL300000037298 none O=C([O-])C1=C(Br)C=CC=C1C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 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, 6, 4, 7, 6, 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, 1, 1, 1, 4, 6, 6, 6] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 22, 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/7769618/working/building/REAL300000037298 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037298
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037298/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037298
Building REAL300000037299
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037299'
/scratch/stefan/7769618/working/building/REAL300000037299 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037299

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037299/0 /scratch/stefan/7769618/working/building/REAL300000037299 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/313
`/scratch/stefan/7769618/working/3D/313' -> `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=NN1CC(=O)NC1=O)

`REAL300000037299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037299 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [43, 31, 31, 31, 31, 31, 39, 31, 31, 31, 31, 31, 31, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 31, 39, 39, 39, 31, 31, 9, 1, 1, 1] 45
rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300000037299 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1CC(=O)NC1=O 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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 11, 31, 31, 31, 31, 31, 31, 3, 3, 3, 1, 3, 3, 3, 1, 1, 11, 31, 31, 31] 45
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 33, 28] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037299 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037299
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037299/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037299
Building REAL300000037300
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037300'
/scratch/stefan/7769618/working/building/REAL300000037300 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037300

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037300/0 /scratch/stefan/7769618/working/building/REAL300000037300 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/314
`/scratch/stefan/7769618/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=O)C=C1Cl)

`REAL300000037300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037300 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 121, 42, 15, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 201, 201, 42, 42, 8, 1, 1, 1, 42] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 657
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: REAL300000037300 none O=C([O-])COC1=CC=C(C=NN2CC(=O)NC2=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 16, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 63, 9, 1, 1, 1, 1, 1, 1, 10, 10, 42, 42, 42, 42, 42, 42, 1, 1, 1, 41, 41, 1, 1, 10, 42, 42, 42, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28])
total number of confs: 266
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037300 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037300
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037300/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037300
Building REAL300000037301
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037301'
/scratch/stefan/7769618/working/building/REAL300000037301 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037301

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037301/0 /scratch/stefan/7769618/working/building/REAL300000037301 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/315
`/scratch/stefan/7769618/working/3D/315' -> `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=NN2CC(=O)NC2=O)C=C1)

`REAL300000037301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037301 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 7, 6, 7, 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, 7, 6, 4, 7, 6, 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, 47, 27, 8, 27, 27, 8, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 57, 57, 47, 27, 27, 8, 1, 1, 1, 27, 27] 57
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
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: REAL300000037301 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2CC(=O)NC2=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.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 1, 7, 7, 6, 7, 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, 7, 6, 4, 7, 6, 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: [14, 11, 14, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 27, 1, 1, 11, 11, 5, 1, 1, 9, 27, 27, 27, 1, 1] 57
rigid atoms, others: [32, 33, 5, 8, 9, 10, 11, 12, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037301 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037301
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037301/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037301
Building REAL300000037302
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037302'
/scratch/stefan/7769618/working/building/REAL300000037302 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037302

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037302/0 /scratch/stefan/7769618/working/building/REAL300000037302 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/316
`/scratch/stefan/7769618/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NN3CC(=O)NC3=O)C(F)=CC=C2S1)

`REAL300000037302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037302 none O=C([O-])C1=CC2=C(C=NN3CC(=O)NC3=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 13, 13] 13
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 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: REAL300000037302 none O=C([O-])C1=CC2=C(C=NN3CC(=O)NC3=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.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 8, 1, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037302 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037302
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037302/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037302
Building REAL300000037303
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037303'
/scratch/stefan/7769618/working/building/REAL300000037303 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037303

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037303/0 /scratch/stefan/7769618/working/building/REAL300000037303 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/317
`/scratch/stefan/7769618/working/3D/317' -> `0.mol2'
Preparing input files

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

`REAL300000037303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037303 none O=C([O-])COC1=CC=CC=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 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, 135, 60, 60, 60, 40, 60, 60, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 60, 60, 60, 60, 24, 24, 1, 1] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 667
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037303 none O=C([O-])COC1=CC=CC=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 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: [45, 24, 45, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 37, 38, 60, 60, 60, 60, 60, 60, 24, 24, 1, 1, 1, 1, 6, 6, 60, 60] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037303 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037303
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037303/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037303
Building REAL300000037304
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037304'
/scratch/stefan/7769618/working/building/REAL300000037304 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037304

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037304/0 /scratch/stefan/7769618/working/building/REAL300000037304 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/318
`/scratch/stefan/7769618/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000037304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037304 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 50, 50, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 7, 117, 117, 1, 1, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 35, 36, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037304 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 1, 15, 124, 123, 201, 201, 201, 201, 201, 201, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 15, 15, 15, 201, 201, 12, 12, 1, 1, 12, 12] 201
rigid atoms, others: [34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 329
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037304 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 58, 117, 117, 66, 67, 201, 201, 201, 201, 201, 201, 201, 117, 117, 58, 58, 58, 58, 1, 1, 117, 117, 201, 201, 117, 117] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037304 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037304
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037304/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037304
Building REAL300000037305
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037305'
/scratch/stefan/7769618/working/building/REAL300000037305 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037305

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037305/0 /scratch/stefan/7769618/working/building/REAL300000037305 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/319
`/scratch/stefan/7769618/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CN=CC(Cl)=N2)=CC=C1OCC(=O)[O-])

`REAL300000037305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037305 none COC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [95, 53, 53, 53, 15, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 126, 201, 201, 201, 95, 95, 95, 53, 15, 15, 1, 1, 53, 53, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037305 none COC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 6, 44, 44, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 9, 20, 26, 26, 3, 3, 3, 1, 6, 6, 53, 53, 1, 1, 20, 20] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037305 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037305
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037305/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037305
Building REAL300000037306
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037306'
/scratch/stefan/7769618/working/building/REAL300000037306 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037306

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037306/0 /scratch/stefan/7769618/working/building/REAL300000037306 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/320
`/scratch/stefan/7769618/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1)

`REAL300000037306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037306 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 200, 201, 154, 89, 22, 91, 91, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 200, 200, 91, 91, 21, 21, 1, 1, 91, 91] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037306 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [18, 9, 18, 3, 1, 1, 1, 1, 1, 1, 8, 54, 54, 91, 91, 91, 91, 91, 91, 1, 1, 9, 9, 1, 1, 8, 8, 91, 91, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037306 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037306
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037306/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037306
Building REAL300000037307
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037307'
/scratch/stefan/7769618/working/building/REAL300000037307 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037307

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037307/0 /scratch/stefan/7769618/working/building/REAL300000037307 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/321
`/scratch/stefan/7769618/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000037307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037307 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 30, 30, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 7, 21, 34, 34, 1, 8, 8, 8, 8, 54, 54, 1, 1, 1, 21, 21, 1] 201
rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 195
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: REAL300000037307 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 54, 54, 54, 54, 54, 142, 201, 201, 201, 54, 23, 23, 23, 23, 1, 1, 54, 54, 54, 201, 201, 54] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 549
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037307 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037307
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037307/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037307
Building REAL300000037308
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037308'
/scratch/stefan/7769618/working/building/REAL300000037308 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037308

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037308/0 /scratch/stefan/7769618/working/building/REAL300000037308 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/322
`/scratch/stefan/7769618/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000037308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037308 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
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, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 18, 18, 1, 1, 5, 5, 5, 5, 62, 62, 1, 1, 9, 17, 17, 1, 1] 187
rigid atoms, others: [32, 1, 36, 37, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35])
total number of confs: 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: REAL300000037308 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
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: [31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 62, 62, 31, 31, 106, 106, 106, 179, 187, 187, 187, 62, 62, 31, 31, 31, 31, 1, 1, 62, 62, 179, 187, 187, 62, 62] 187
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 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])
total number of confs: 857
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037308 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037308
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037308/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037308
Building REAL300000037309
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037309'
/scratch/stefan/7769618/working/building/REAL300000037309 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037309

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037309/0 /scratch/stefan/7769618/working/building/REAL300000037309 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/323
`/scratch/stefan/7769618/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1)

`REAL300000037309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037309 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 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, 7, 7, 3, 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]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 21, 21, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 5, 36, 36, 1, 1, 9, 9, 9, 9, 9, 1, 1] 103
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037309 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 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, 7, 7, 3, 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]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 36, 36, 20, 20, 52, 52, 52, 103, 103, 103, 103, 103, 36, 36, 20, 20, 20, 20, 1, 1, 36, 36, 103, 103, 103, 103, 103, 36, 36] 103
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 424
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037309 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037309
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037309/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037309
Building REAL300000037310
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037310'
/scratch/stefan/7769618/working/building/REAL300000037310 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037310

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037310/0 /scratch/stefan/7769618/working/building/REAL300000037310 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/324
`/scratch/stefan/7769618/working/3D/324' -> `0.mol2'
Preparing input files

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

`REAL300000037310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037310 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
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, 1, 1, 5, 5, 5, 5, 1, 1] 13
rigid atoms, others: [1, 34, 33, 40, 11, 12, 13, 14, 15, 25, 26, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 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: REAL300000037310 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 5, 8, 8, 8, 13, 13, 13, 13, 13, 13, 5, 5, 3, 3, 3, 3, 1, 1, 5, 5, 13, 13, 13, 13, 5, 5] 13
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037310 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037310
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037310/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037310
Building REAL300000037311
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037311'
/scratch/stefan/7769618/working/building/REAL300000037311 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037311

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037311/0 /scratch/stefan/7769618/working/building/REAL300000037311 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/325
`/scratch/stefan/7769618/working/3D/325' -> `0.mol2'
Preparing input files

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

`REAL300000037311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037311 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 5, 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, 7, 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]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 44, 44, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 7, 82, 82, 1, 1, 2, 2, 1, 1] 117
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 19, 20, 27, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 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: REAL300000037311 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 5, 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, 7, 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]
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: [44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 44, 82, 82, 47, 73, 117, 117, 117, 82, 82, 44, 44, 44, 44, 1, 1, 82, 82, 117, 117, 82, 82] 117
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 568
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037311 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037311
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037311/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037311
Building REAL300000037312
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037312'
/scratch/stefan/7769618/working/building/REAL300000037312 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037312

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037312/0 /scratch/stefan/7769618/working/building/REAL300000037312 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/326
`/scratch/stefan/7769618/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CN=CC(Cl)=N1)CCC2)

`REAL300000037312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037312 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1, 26, 26, 26, 26, 26, 26] 26
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
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: REAL300000037312 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 1, 26, 26, 1, 1, 1, 1, 1, 1] 26
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 19, 20, 21, 25, 28, 29, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037312 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037312/1 /scratch/stefan/7769618/working/building/REAL300000037312 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/327
`/scratch/stefan/7769618/working/3D/327' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CN=CC(Cl)=N1)CCC2)

`REAL300000037312.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037312/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037312 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 3, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 3, 1, 1, 9, 9, 9, 9, 9, 9] 9
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
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: REAL300000037312 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 3, 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, 3, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 8, 9, 9, 1, 1, 1, 1, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 28, 29, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27])
total number of confs: 31
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037312 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037312
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037312/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037312/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037312
Building REAL300000037313
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037313'
/scratch/stefan/7769618/working/building/REAL300000037313 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037313

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037313/0 /scratch/stefan/7769618/working/building/REAL300000037313 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/328
`/scratch/stefan/7769618/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1)

`REAL300000037313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037313 none O=C([O-])CCOC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 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, 200, 201, 200, 181, 87, 26, 89, 89, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 200, 200, 200, 200, 89, 89, 23, 23, 1, 1, 89, 89] 201
rigid atoms, others: [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, 32, 33])
total number of confs: 609
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: REAL300000037313 none O=C([O-])CCOC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 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: [15, 11, 15, 11, 3, 1, 1, 1, 1, 1, 1, 8, 52, 52, 89, 89, 89, 89, 89, 89, 1, 1, 11, 11, 11, 11, 1, 1, 8, 8, 89, 89, 1, 1] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 196
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037313 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037313
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037313/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037313
Building REAL300000037314
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037314'
/scratch/stefan/7769618/working/building/REAL300000037314 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037314

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037314/0 /scratch/stefan/7769618/working/building/REAL300000037314 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/329
`/scratch/stefan/7769618/working/3D/329' -> `0.mol2'
Preparing input files

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

`REAL300000037314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037314 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 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, 201, 201, 131, 58, 58, 58, 22, 58, 58, 58, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 58, 58, 58, 22, 22, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 29, 30] 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: 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: REAL300000037314 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 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: [44, 23, 44, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 37, 38, 58, 58, 58, 58, 58, 58, 23, 23, 1, 1, 1, 6, 6, 58, 58] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037314 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037314
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037314/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037314
Building REAL300000037315
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037315'
/scratch/stefan/7769618/working/building/REAL300000037315 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037315

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037315/0 /scratch/stefan/7769618/working/building/REAL300000037315 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/330
`/scratch/stefan/7769618/working/3D/330' -> `0.mol2'
Preparing input files

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

`REAL300000037315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037315 none CC(OC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 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: [201, 152, 58, 58, 58, 58, 58, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 16, 16, 1, 1, 58] 201
rigid atoms, others: [32, 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, 33])
total number of confs: 517
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037315 none CC(OC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 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: [20, 9, 1, 1, 1, 1, 1, 1, 1, 7, 44, 44, 58, 58, 58, 58, 58, 58, 1, 20, 25, 25, 20, 20, 20, 20, 1, 1, 1, 7, 7, 58, 58, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 173
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037315 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037315
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037315/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037315
Building REAL300000037316
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037316'
/scratch/stefan/7769618/working/building/REAL300000037316 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037316

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037316/0 /scratch/stefan/7769618/working/building/REAL300000037316 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/331
`/scratch/stefan/7769618/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)

`REAL300000037316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037316 none O=C([O-])CCOC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 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, 199, 59, 59, 59, 59, 59, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 59, 59, 59, 16, 16, 1, 1, 59] 201
rigid atoms, others: [32, 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, 33])
total number of confs: 310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037316 none O=C([O-])CCOC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 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: [17, 10, 17, 10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 38, 39, 59, 59, 59, 59, 59, 59, 1, 10, 10, 10, 10, 1, 1, 1, 6, 6, 59, 59, 1] 201
rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037316 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037316
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037316/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037316
Building REAL300000037317
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037317'
/scratch/stefan/7769618/working/building/REAL300000037317 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037317

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037317/0 /scratch/stefan/7769618/working/building/REAL300000037317 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/332
`/scratch/stefan/7769618/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)

`REAL300000037317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037317 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 9, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 64, 65, 103, 103, 103, 103, 103, 103, 1, 6, 6, 6, 6, 2, 2, 1, 1, 1, 8, 8, 103, 103, 1] 201
rigid atoms, others: [33, 34, 35, 40, 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])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037317 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 168, 167, 102, 102, 102, 102, 102, 20, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 167, 167, 102, 102, 102, 20, 20, 1, 1, 102] 201
rigid atoms, others: [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, 37, 40])
total number of confs: 355
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037317 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 31, 142, 143, 201, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 31, 31, 201, 201, 6] 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])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037317 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037317
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037317/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037317
Building REAL300000037318
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037318'
/scratch/stefan/7769618/working/building/REAL300000037318 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037318

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037318/0 /scratch/stefan/7769618/working/building/REAL300000037318 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/333
`/scratch/stefan/7769618/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-])

`REAL300000037318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037318 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 15, 15, 9, 4, 4, 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, 9] 15
rigid atoms, others: [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, 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: REAL300000037318 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 5, 5, 1, 1, 6, 8, 9, 9, 1] 15
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037318 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037318/1 /scratch/stefan/7769618/working/building/REAL300000037318 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/334
`/scratch/stefan/7769618/working/3D/334' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-])

`REAL300000037318.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037318/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037318 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 187, 31, 22, 90, 90, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 201, 201, 90, 90, 22, 22, 1, 1, 90] 201
rigid atoms, others: [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, 32])
total number of confs: 538
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037318 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 17, 21, 7, 1, 1, 1, 1, 1, 1, 8, 53, 53, 90, 90, 90, 90, 90, 90, 1, 1, 1, 2, 2, 17, 17, 1, 1, 8, 8, 90, 90, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037318 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037318
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037318/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037318/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037318
Building REAL300000037319
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037319'
/scratch/stefan/7769618/working/building/REAL300000037319 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037319

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037319/0 /scratch/stefan/7769618/working/building/REAL300000037319 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/335
`/scratch/stefan/7769618/working/3D/335' -> `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=CN=CC(Cl)=N3)C=C2)=C1)

`REAL300000037319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037319 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 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, 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: [6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 46, 46, 82, 82, 82, 82, 82, 82, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 82, 82, 1, 1, 6] 201
rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 13, 14, 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, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037319 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 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, 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, 201, 82, 82, 80, 17, 82, 82, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 201, 201, 82, 82, 82, 82, 16, 16, 1, 1, 82, 82, 201] 201
rigid atoms, others: [36, 37, 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, 38, 39, 40])
total number of confs: 492
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037319 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 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, 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: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 31, 151, 151, 201, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 31, 31, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 40, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037319 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037319
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037319/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037319
Building REAL300000037320
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037320'
/scratch/stefan/7769618/working/building/REAL300000037320 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037320

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037320/0 /scratch/stefan/7769618/working/building/REAL300000037320 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/336
`/scratch/stefan/7769618/working/3D/336' -> `0.mol2'
Preparing input files

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

`REAL300000037320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037320 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC(Cl)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 10, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 49, 49, 49, 49, 49, 49, 1, 11, 10, 11, 11, 2, 2, 1, 1, 1, 7, 7, 49, 49, 1, 11] 201
rigid atoms, others: [32, 33, 34, 39, 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, 40])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037320 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC(Cl)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 84, 84, 49, 49, 49, 49, 49, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 84, 84, 49, 49, 49, 16, 16, 1, 1, 49, 201] 201
rigid atoms, others: [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, 36, 39, 40])
total number of confs: 333
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037320 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC(Cl)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 54, 191, 191, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 6, 6, 11, 11, 11, 54, 54, 201, 201, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 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])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037320 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037320
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037320/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037320
Building REAL300000037321
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037321'
/scratch/stefan/7769618/working/building/REAL300000037321 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037321

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037321/0 /scratch/stefan/7769618/working/building/REAL300000037321 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/337
`/scratch/stefan/7769618/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)

`REAL300000037321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037321 none O=C([O-])COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 159, 61, 61, 61, 61, 61, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 61, 61, 61, 18, 18, 1, 1, 61] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 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: REAL300000037321 none O=C([O-])COC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 16, 29, 6, 1, 1, 1, 1, 1, 1, 1, 6, 44, 45, 61, 61, 61, 61, 61, 61, 1, 16, 16, 1, 1, 1, 6, 6, 61, 61, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037321 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037321
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037321/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037321
Building REAL300000037322
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037322'
/scratch/stefan/7769618/working/building/REAL300000037322 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037322

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037322/0 /scratch/stefan/7769618/working/building/REAL300000037322 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/338
`/scratch/stefan/7769618/working/3D/338' -> `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=CN=CC(Cl)=N3)C=C2)OC=C1)

`REAL300000037322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037322 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 8, 64, 64, 134, 134, 134, 134, 134, 134, 1, 1, 7, 7, 7, 3, 3, 1, 1, 8, 8, 134, 134, 1, 1, 7, 7] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36, 37])
total number of confs: 227
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037322 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 140, 134, 132, 34, 134, 134, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 140, 140, 134, 134, 32, 32, 1, 1, 134, 134, 201, 201] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37])
total number of confs: 654
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037322 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 5, 7, 7, 7, 7, 7, 38, 169, 170, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 5, 5, 7, 7, 38, 38, 201, 201, 7, 7, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 23, 24, 25, 37, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 361
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037322 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037322
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037322/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037322
Building REAL300000037323
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037323'
/scratch/stefan/7769618/working/building/REAL300000037323 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037323

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037323/0 /scratch/stefan/7769618/working/building/REAL300000037323 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/339
`/scratch/stefan/7769618/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C(OCC(=O)[O-])=C1)

`REAL300000037323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037323 none COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 5, 1, 11, 11, 1, 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, 3, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 67, 37, 67, 67, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 129, 197, 201, 201, 67, 83, 83, 83, 67, 67, 24, 24, 1, 1, 197, 197, 67] 201
rigid atoms, others: [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, 32, 33, 34])
total number of confs: 728
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037323 none COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 5, 1, 11, 11, 1, 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, 3, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 39, 39, 67, 67, 67, 67, 67, 67, 1, 1, 7, 19, 38, 38, 1, 3, 3, 3, 1, 1, 6, 6, 67, 67, 19, 19, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037323 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037323
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037323/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037323
Building REAL300000037324
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037324'
/scratch/stefan/7769618/working/building/REAL300000037324 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037324

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037324/0 /scratch/stefan/7769618/working/building/REAL300000037324 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/340
`/scratch/stefan/7769618/working/3D/340' -> `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=CN=CC(Cl)=N2)C=C1)

`REAL300000037324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037324 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 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, 140, 201, 201, 56, 18, 57, 57, 15, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 15, 15, 1, 1, 57, 57] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 29, 30])
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: REAL300000037324 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 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: [21, 17, 21, 6, 17, 17, 1, 1, 1, 1, 1, 1, 6, 45, 45, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 6, 6, 57, 57, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037324 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037324
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037324/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037324
Building REAL300000037325
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037325'
/scratch/stefan/7769618/working/building/REAL300000037325 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037325

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037325/0 /scratch/stefan/7769618/working/building/REAL300000037325 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/341
`/scratch/stefan/7769618/working/3D/341' -> `0.mol2'
Preparing input files

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

`REAL300000037325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037325 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 70, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 34, 34, 1, 1] 70
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25])
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: REAL300000037325 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 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, 2, 2, 1, 1, 1, 1, 1, 8, 42, 42, 70, 70, 70, 70, 70, 70, 2, 2, 2, 1, 8, 8, 70, 70] 70
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037325 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037325
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037325/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037325
Building REAL300000037326
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037326'
/scratch/stefan/7769618/working/building/REAL300000037326 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037326

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037326/0 /scratch/stefan/7769618/working/building/REAL300000037326 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/342
`/scratch/stefan/7769618/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1Br)

`REAL300000037326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037326 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 187, 87, 37, 88, 88, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 201, 201, 88, 88, 21, 21, 1, 1, 88] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 589
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037326 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [22, 17, 22, 7, 1, 1, 1, 1, 1, 1, 7, 49, 49, 88, 88, 88, 88, 88, 88, 1, 1, 1, 17, 17, 1, 1, 7, 7, 88, 88, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037326 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037326
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037326/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037326
Building REAL300000037327
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037327'
/scratch/stefan/7769618/working/building/REAL300000037327 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037327

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037327/0 /scratch/stefan/7769618/working/building/REAL300000037327 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/343
`/scratch/stefan/7769618/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC(Cl)=N2)C=C1)

`REAL300000037327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037327 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 52, 52, 1, 1, 155, 155] 155
rigid atoms, others: [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, 32, 33])
total number of confs: 302
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037327 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 64, 64, 155, 155, 155, 155, 155, 155, 1, 1, 4, 4, 4, 1, 8, 8, 155, 155, 1, 1] 155
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 22, 23, 27] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037327 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037327/1 /scratch/stefan/7769618/working/building/REAL300000037327 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/344
`/scratch/stefan/7769618/working/3D/344' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC(Cl)=N2)C=C1)

`REAL300000037327.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037327/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037327 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 13, 4, 1, 1, 21, 21] 21
rigid atoms, others: [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, 32, 33])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037327 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 19, 21, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 1, 8, 19, 21, 21, 1, 1] 21
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 22, 23, 27] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037327 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037327
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037327/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037327/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037327
Building REAL300000037328
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037328'
/scratch/stefan/7769618/working/building/REAL300000037328 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037328

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037328/0 /scratch/stefan/7769618/working/building/REAL300000037328 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/345
`/scratch/stefan/7769618/working/3D/345' -> `0.mol2'
Preparing input files

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

`REAL300000037328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037328 none CCC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 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, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 1, 6, 31, 31, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 10, 10, 6, 52, 52, 1, 1, 1, 1] 56
rigid atoms, others: [32, 2, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 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: REAL300000037328 none CCC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 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, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [46, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 33, 52, 52, 33, 46, 52, 52, 52, 52, 48, 48, 48, 48, 48, 33, 1, 1, 52, 52, 52, 52] 56
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037328 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037328
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037328/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037328
Building REAL300000037329
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037329'
/scratch/stefan/7769618/working/building/REAL300000037329 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037329

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037329/0 /scratch/stefan/7769618/working/building/REAL300000037329 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/346
`/scratch/stefan/7769618/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000037329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037329 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 42, 42, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 60, 60, 1, 1, 1, 2] 120
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 106
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: REAL300000037329 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 60, 60, 60, 60, 60, 60, 60, 60, 60, 31, 31, 31, 31, 1, 1, 60, 60, 60, 120] 120
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 260
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037329 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037329/1 /scratch/stefan/7769618/working/building/REAL300000037329 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/347
`/scratch/stefan/7769618/working/3D/347' -> `1.mol2'
Preparing input files

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

`REAL300000037329.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037329/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037329 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 1, 1, 1, 2] 52
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 71
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: REAL300000037329 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 4, 1, 1, 26, 26, 26, 52] 52
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 94
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037329 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037329
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037329/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037329/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037329
Building REAL300000037330
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037330'
/scratch/stefan/7769618/working/building/REAL300000037330 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037330

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037330/0 /scratch/stefan/7769618/working/building/REAL300000037330 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/348
`/scratch/stefan/7769618/working/3D/348' -> `0.mol2'
Preparing input files

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

`REAL300000037330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037330 none CCC(N=NC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 1, 11, 61, 61, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 21, 11, 120, 120, 1, 1, 1] 141
rigid atoms, others: [32, 2, 12, 13, 14, 15, 18, 19, 20, 21, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037330 none CCC(N=NC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [61, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 47, 120, 120, 120, 120, 120, 120, 120, 120, 120, 73, 73, 73, 73, 73, 47, 1, 1, 120, 120, 120] 141
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32])
total number of confs: 459
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037330 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037330
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037330/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037330
Building REAL300000037331
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037331'
/scratch/stefan/7769618/working/building/REAL300000037331 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037331

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037331/0 /scratch/stefan/7769618/working/building/REAL300000037331 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/349
`/scratch/stefan/7769618/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(CN=NC3=CN=CC(Cl)=N3)=C2C=C1)

`REAL300000037331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037331 none O=C([O-])C1=CC2=NNC(CN=NC3=CN=CC(Cl)=N3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 34, 34, 1, 1, 90, 90] 90
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 28, 29])
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: REAL300000037331 none O=C([O-])C1=CC2=NNC(CN=NC3=CN=CC(Cl)=N3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 57, 57, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 9, 9, 90, 90, 1, 1] 90
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037331 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037331
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037331/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037331
Building REAL300000037332
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037332'
/scratch/stefan/7769618/working/building/REAL300000037332 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037332

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037332/0 /scratch/stefan/7769618/working/building/REAL300000037332 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/350
`/scratch/stefan/7769618/working/3D/350' -> `0.mol2'
Preparing input files

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

`REAL300000037332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037332 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 13, 73, 73, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 13, 155, 155, 1, 1, 1] 155
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26])
total number of confs: 248
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037332 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [57, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 57, 155, 155, 155, 155, 155, 155, 155, 155, 155, 57, 57, 57, 57, 1, 1, 155, 155, 155] 155
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037332 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037332/1 /scratch/stefan/7769618/working/building/REAL300000037332 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/351
`/scratch/stefan/7769618/working/3D/351' -> `1.mol2'
Preparing input files

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

`REAL300000037332.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037332/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037332 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 39, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 39, 53, 53, 1, 1, 1] 53
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26])
total number of confs: 129
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037332 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 53, 53, 53, 53, 53, 53, 53, 53, 53, 18, 18, 18, 4, 1, 1, 53, 53, 53] 53
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29])
total number of confs: 78
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037332 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037332
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037332/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037332/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037332
Building REAL300000037333
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037333'
/scratch/stefan/7769618/working/building/REAL300000037333 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037333

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037333/0 /scratch/stefan/7769618/working/building/REAL300000037333 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/352
`/scratch/stefan/7769618/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CN=CC(Cl)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000037333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037333 none COC1=CC(C=NNC2=CN=CC(Cl)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [63, 38, 38, 38, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 83, 108, 108, 108, 63, 63, 63, 38, 14, 4, 1, 1, 38, 108, 108] 108
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 310
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: REAL300000037333 none COC1=CC(C=NNC2=CN=CC(Cl)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1, 1, 9, 17, 25, 25, 4, 4, 4, 1, 7, 25, 38, 38, 1, 17, 17] 108
rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 35, 36])
total number of confs: 175
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037333 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037333
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037333/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037333
Building REAL300000037334
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037334'
/scratch/stefan/7769618/working/building/REAL300000037334 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037334

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037334/0 /scratch/stefan/7769618/working/building/REAL300000037334 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/353
`/scratch/stefan/7769618/working/3D/353' -> `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=CN=CC(Cl)=N1)

`REAL300000037334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037334 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 114, 150, 201, 201, 201, 114, 114, 114, 114, 114, 114, 114, 114, 114, 46, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 201, 201, 114, 114, 114, 46, 46, 1, 1] 201
rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 635
number of broken/clashed sets: 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: REAL300000037334 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 14, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 49, 50, 114, 114, 114, 114, 114, 114, 4, 4, 4, 14, 14, 1, 1, 1, 7, 7, 114, 114] 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])
total number of confs: 253
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037334 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037334
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037334/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037334
Building REAL300000037335
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037335'
/scratch/stefan/7769618/working/building/REAL300000037335 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037335

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037335/0 /scratch/stefan/7769618/working/building/REAL300000037335 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/354
`/scratch/stefan/7769618/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000037335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037335 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 23, 23, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 19, 19, 9, 11, 19, 19, 19, 19, 1, 1, 5, 5, 5, 5, 53, 53, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 33, 40, 11, 12, 13, 14, 15, 25, 26, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 160
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037335 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 19, 46, 154, 154, 201, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 46, 46, 46, 46, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 391
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037335 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 1, 24, 53, 53, 39, 53, 183, 201, 201, 183, 183, 201, 201, 201, 201, 53, 53, 24, 24, 24, 24, 1, 1, 53, 53, 201, 201, 201, 201, 53, 53] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037335 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037335
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037335/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037335
Building REAL300000037336
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037336'
/scratch/stefan/7769618/working/building/REAL300000037336 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037336

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037336/0 /scratch/stefan/7769618/working/building/REAL300000037336 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/355
`/scratch/stefan/7769618/working/3D/355' -> `0.mol2'
Preparing input files

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

`REAL300000037336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037336 none COC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 63, 63, 63, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 156, 190, 190, 201, 194, 104, 104, 104, 63, 16, 16, 1, 1, 63, 63, 190, 190, 190, 190] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37])
total number of confs: 560
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037336 none COC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 7, 11, 11, 19, 17, 3, 3, 3, 1, 6, 6, 63, 63, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037336 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037336
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037336/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037336
Building REAL300000037337
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037337'
/scratch/stefan/7769618/working/building/REAL300000037337 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037337

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037337/0 /scratch/stefan/7769618/working/building/REAL300000037337 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/356
`/scratch/stefan/7769618/working/3D/356' -> `0.mol2'
Preparing input files

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

`REAL300000037337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037337 none O=C([O-])C1=CC=C(CN=NC2=CN=CC(Cl)=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 68, 69, 37, 69, 69, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 33, 33, 1, 1, 69] 69
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 26])
total number of confs: 284
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037337 none O=C([O-])C1=CC=C(CN=NC2=CN=CC(Cl)=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 44, 44, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 8, 8, 69, 69, 1] 69
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037337 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037337/1 /scratch/stefan/7769618/working/building/REAL300000037337 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/357
`/scratch/stefan/7769618/working/3D/357' -> `1.mol2'
Preparing input files

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

`REAL300000037337.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037337/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037337 none O=C([O-])C1=CC=C(C=NNC2=CN=CC(Cl)=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 8, 4, 1, 1, 10] 10
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 26])
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: REAL300000037337 none O=C([O-])C1=CC=C(C=NNC2=CN=CC(Cl)=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 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/7769618/working/building/REAL300000037337 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037337
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037337/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037337/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037337
Building REAL300000037338
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037338'
/scratch/stefan/7769618/working/building/REAL300000037338 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037338

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037338/0 /scratch/stefan/7769618/working/building/REAL300000037338 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/358
`/scratch/stefan/7769618/working/3D/358' -> `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=CN=CC(Cl)=N1)

`REAL300000037338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037338 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=N1 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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 7, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 25, 25, 25, 25, 1, 1] 39
rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
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: REAL300000037338 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=N1 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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 26, 26, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 39, 39] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037338 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037338/1 /scratch/stefan/7769618/working/building/REAL300000037338 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/359
`/scratch/stefan/7769618/working/3D/359' -> `1.mol2'
Preparing input files

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

`REAL300000037338.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037338/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037338 none CC(=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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]
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: [9, 1, 9, 9, 31, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 31, 38, 38, 1, 2, 2, 2, 2, 2, 2] 38
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 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: REAL300000037338 none CC(=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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]
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: [17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 17, 17, 4, 1, 1, 38, 38, 38, 38, 38, 38, 38] 38
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 57
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037338 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037338
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037338/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037338/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037338
Building REAL300000037339
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037339'
/scratch/stefan/7769618/working/building/REAL300000037339 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037339

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037339/0 /scratch/stefan/7769618/working/building/REAL300000037339 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/360
`/scratch/stefan/7769618/working/3D/360' -> `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=CN=CC(Cl)=N1)

`REAL300000037339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037339 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=N1 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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 5, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 23, 23, 23, 23, 1, 1] 37
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037339 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=N1 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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 37, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 37, 37] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037339 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037339/1 /scratch/stefan/7769618/working/building/REAL300000037339 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/361
`/scratch/stefan/7769618/working/3D/361' -> `1.mol2'
Preparing input files

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

`REAL300000037339.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037339/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037339 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 1, 1, 1, 2, 2, 2] 19
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 59
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037339 none CC(=NNC1=CN=CC(Cl)=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
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: [13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 4, 1, 1, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 33
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037339 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037339
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037339/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037339/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037339
Building REAL300000037340
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037340'
/scratch/stefan/7769618/working/building/REAL300000037340 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037340

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037340/0 /scratch/stefan/7769618/working/building/REAL300000037340 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/362
`/scratch/stefan/7769618/working/3D/362' -> `0.mol2'
Preparing input files

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

`REAL300000037340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037340 none CC(OC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 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: [201, 152, 38, 21, 83, 83, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 201, 201, 83, 83, 21, 21, 1, 1, 83, 83] 201
rigid atoms, others: [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, 32, 33])
total number of confs: 699
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037340 none CC(OC1=CC=C(CN=NC2=CN=CC(Cl)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 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: [13, 6, 1, 1, 1, 1, 1, 1, 7, 51, 51, 83, 83, 83, 83, 83, 83, 1, 1, 13, 18, 18, 13, 13, 13, 13, 1, 1, 7, 7, 83, 83, 1, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 18, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 192
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037340 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037340
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037340/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037340
Building REAL300000037341
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037341'
/scratch/stefan/7769618/working/building/REAL300000037341 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037341

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037341/0 /scratch/stefan/7769618/working/building/REAL300000037341 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/363
`/scratch/stefan/7769618/working/3D/363' -> `0.mol2'
Preparing input files

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

`REAL300000037341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037341 none O=C([O-])C1CCC(N=NC2=CN=CC(Cl)=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 11, 11, 11, 11] 11
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
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: REAL300000037341 none O=C([O-])C1CCC(N=NC2=CN=CC(Cl)=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037341 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037341
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037341/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037341
Building REAL300000037342
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037342'
/scratch/stefan/7769618/working/building/REAL300000037342 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037342

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037342/0 /scratch/stefan/7769618/working/building/REAL300000037342 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/364
`/scratch/stefan/7769618/working/3D/364' -> `0.mol2'
Preparing input files

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

`REAL300000037342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037342 none O=C([O-])CN1C=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 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, 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, 109, 109, 109, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 201, 201, 109, 30, 30, 1, 1, 109, 109, 109, 109] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 668
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037342 none O=C([O-])CN1C=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 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, 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: [12, 8, 12, 1, 1, 1, 1, 1, 8, 63, 64, 109, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 109, 109, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037342 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037342
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037342/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037342
Building REAL300000037343
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037343'
/scratch/stefan/7769618/working/building/REAL300000037343 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037343

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037343/0 /scratch/stefan/7769618/working/building/REAL300000037343 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/365
`/scratch/stefan/7769618/working/3D/365' -> `0.mol2'
Preparing input files

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

`REAL300000037343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037343 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 34, 1, 1, 1, 1, 1, 1, 6, 15, 17, 28, 43, 43, 1, 5, 5, 5, 5, 34, 34, 1, 1, 1, 15, 15, 17, 17, 28, 28, 1] 201
rigid atoms, others: [32, 1, 39, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 243
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: REAL300000037343 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 34, 34, 34, 34, 34, 124, 155, 156, 201, 201, 201, 34, 10, 10, 10, 10, 1, 1, 34, 34, 34, 155, 155, 156, 156, 201, 201, 34] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 626
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037343 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037343
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037343/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037343
Building REAL300000037344
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037344'
/scratch/stefan/7769618/working/building/REAL300000037344 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037344

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037344/0 /scratch/stefan/7769618/working/building/REAL300000037344 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/366
`/scratch/stefan/7769618/working/3D/366' -> `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=CN=CC(Cl)=N1)

`REAL300000037344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037344 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 7, 27, 54, 58, 58, 58, 58, 58, 171, 201, 201, 201, 201, 58, 58, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 56, 56, 57, 58, 58, 58, 201, 201, 201, 201, 58, 58, 1, 1] 201
rigid atoms, others: [41, 42, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 562
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037344 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 24, 35, 35, 1, 1, 8, 32, 32, 58, 58, 58, 58, 58, 58, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 24, 24, 24, 24, 1, 1, 58, 58] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42])
total number of confs: 217
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037344 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037344
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037344/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037344
Building REAL300000037345
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037345'
/scratch/stefan/7769618/working/building/REAL300000037345 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037345

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037345/0 /scratch/stefan/7769618/working/building/REAL300000037345 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/367
`/scratch/stefan/7769618/working/3D/367' -> `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=CN=CC(Cl)=N1)

`REAL300000037345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037345 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 64, 64, 64, 64, 146, 201, 201, 201, 64, 64, 7, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 62, 62, 62, 64, 64, 64, 201, 201, 64, 64, 1, 1] 201
rigid atoms, others: [38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 668
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: REAL300000037345 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 37, 1, 1, 9, 36, 36, 64, 64, 64, 64, 64, 64, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 23, 22, 1, 1, 64, 64] 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])
total number of confs: 230
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037345 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037345
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037345/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037345
Building REAL300000037346
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037346'
/scratch/stefan/7769618/working/building/REAL300000037346 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037346

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037346/0 /scratch/stefan/7769618/working/building/REAL300000037346 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/368
`/scratch/stefan/7769618/working/3D/368' -> `0.mol2'
Preparing input files

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

`REAL300000037346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037346 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 24, 24, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 10, 26, 26, 34, 34, 1, 6, 6, 6, 6, 48, 48, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 16, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 193
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037346 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 48, 48, 48, 48, 48, 168, 201, 201, 201, 201, 48, 17, 17, 17, 17, 1, 1, 48, 48, 48, 201, 201, 201, 201, 48] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 443
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037346 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037346
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037346/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037346
Building REAL300000037347
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037347'
/scratch/stefan/7769618/working/building/REAL300000037347 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037347

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037347/0 /scratch/stefan/7769618/working/building/REAL300000037347 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/369
`/scratch/stefan/7769618/working/3D/369' -> `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=CN=CC(Cl)=N1)

`REAL300000037347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037347 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 195, 201, 201, 201, 201, 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] 201
rigid atoms, others: [41, 42, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 503
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: REAL300000037347 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 15, 16, 22, 22, 1, 1, 9, 40, 40, 69, 69, 69, 69, 69, 69, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 15, 15, 15, 15, 1, 1, 69, 69] 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])
total number of confs: 195
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037347 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037347
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037347/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037347
Building REAL300000037348
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037348'
/scratch/stefan/7769618/working/building/REAL300000037348 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037348

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037348/0 /scratch/stefan/7769618/working/building/REAL300000037348 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/370
`/scratch/stefan/7769618/working/3D/370' -> `0.mol2'
Preparing input files

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

`REAL300000037348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037348 none CCC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 26, 34, 51, 54, 58, 1, 1, 5, 5, 5, 5, 5, 4, 21, 21, 1, 1, 11, 11, 25, 25, 34, 34, 51, 51, 1, 1] 201
rigid atoms, others: [2, 35, 44, 45, 12, 34, 14, 13, 16, 24, 25, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 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: REAL300000037348 none CCC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 21, 21, 16, 20, 81, 90, 142, 150, 187, 197, 201, 21, 21, 21, 21, 21, 21, 21, 14, 1, 1, 21, 21, 90, 90, 142, 142, 150, 150, 187, 187, 21, 21] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 802
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037348 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037348
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037348/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037348
Building REAL300000037349
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037349'
/scratch/stefan/7769618/working/building/REAL300000037349 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037349

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037349/0 /scratch/stefan/7769618/working/building/REAL300000037349 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/371
`/scratch/stefan/7769618/working/3D/371' -> `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=CN=CC(Cl)=N2)C1)

`REAL300000037349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037349 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 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: [7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 1, 6, 6, 6, 37, 37, 6, 6] 37
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 62
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037349 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 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: [36, 25, 36, 25, 25, 37, 37, 30, 37, 37, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 37, 37, 25, 25, 25, 1, 1, 25, 25] 37
rigid atoms, others: [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, 32, 33])
total number of confs: 149
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037349 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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, 3, 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: [3, 1, 3, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 13, 13, 25, 25, 25, 25, 25, 25, 1, 6, 6, 3, 6, 6, 1, 1, 1, 25, 25, 1, 1] 37
rigid atoms, others: [32, 1, 3, 4, 33, 10, 11, 12, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 57
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037349 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037349
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037349/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037349
Building REAL300000037350
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037350'
/scratch/stefan/7769618/working/building/REAL300000037350 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037350

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037350/0 /scratch/stefan/7769618/working/building/REAL300000037350 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/372
`/scratch/stefan/7769618/working/3D/372' -> `0.mol2'
Preparing input files

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

`REAL300000037350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037350 none CC(N=NC1=CN=CC(Cl)=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 24, 24, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 59, 59, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 78
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 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: REAL300000037350 none CC(N=NC1=CN=CC(Cl)=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 45, 59, 59, 59, 59, 59, 78, 78, 78, 59, 59, 59, 45, 45, 45, 45, 1, 1, 59, 59, 78, 78, 59, 59, 59, 59, 59, 59] 78
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037350 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037350
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037350/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037350
Building REAL300000037351
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037351'
/scratch/stefan/7769618/working/building/REAL300000037351 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037351

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037351/0 /scratch/stefan/7769618/working/building/REAL300000037351 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/373
`/scratch/stefan/7769618/working/3D/373' -> `0.mol2'
Preparing input files

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

`REAL300000037351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037351 none CC1C(N=NC2=CN=CC(Cl)=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
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: REAL300000037351 none CC1C(N=NC2=CN=CC(Cl)=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 17
rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 12, 13, 14, 15, 34, 18, 19, 20, 24, 25, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 38, 16, 17, 21, 22, 23, 36, 26, 27, 37])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037351 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037351
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037351/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037351
Building REAL300000037352
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037352'
/scratch/stefan/7769618/working/building/REAL300000037352 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037352

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037352/0 /scratch/stefan/7769618/working/building/REAL300000037352 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/374
`/scratch/stefan/7769618/working/3D/374' -> `0.mol2'
Preparing input files

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

`REAL300000037352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037352 none COC1=CC(C(C)N=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 41, 41, 41, 13, 4, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 117, 182, 182, 201, 201, 201, 67, 67, 67, 41, 13, 13, 13, 13, 1, 1, 41, 41, 182, 182, 182, 182, 201, 201] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 672
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037352 none COC1=CC(C(C)N=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 22, 22, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 6, 14, 14, 22, 26, 26, 3, 3, 3, 1, 6, 6, 6, 6, 41, 41, 1, 1, 14, 14, 14, 14, 22, 22] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 36, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037352 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037352
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037352/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037352
Building REAL300000037353
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037353'
/scratch/stefan/7769618/working/building/REAL300000037353 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037353

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037353/0 /scratch/stefan/7769618/working/building/REAL300000037353 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/375
`/scratch/stefan/7769618/working/3D/375' -> `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=CN=CC(Cl)=N2)C1)

`REAL300000037353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037353 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 1, 9, 9, 9, 23, 23, 9, 9] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 45
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037353 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [13, 11, 13, 11, 11, 23, 23, 23, 23, 23, 23, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 11, 11, 11, 1, 1, 11, 11] 23
rigid atoms, others: [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, 32, 33])
total number of confs: 47
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037353 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC(Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 1, 9, 9, 9, 9, 1, 1, 1, 11, 11, 1, 1] 23
rigid atoms, others: [32, 1, 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])
total number of confs: 30
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037353 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037353
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037353/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037353
Building REAL300000037354
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037354'
/scratch/stefan/7769618/working/building/REAL300000037354 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037354

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037354/0 /scratch/stefan/7769618/working/building/REAL300000037354 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/376
`/scratch/stefan/7769618/working/3D/376' -> `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=CN=CC(Cl)=N2)C1)

`REAL300000037354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037354 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 9, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 9, 9, 9, 24, 24, 9, 9] 24
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 51
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037354 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [14, 12, 14, 12, 12, 24, 24, 24, 24, 24, 24, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 24, 12, 12, 12, 1, 1, 12, 12] 24
rigid atoms, others: [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, 32, 33])
total number of confs: 51
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037354 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 1, 9, 9, 9, 9, 1, 1, 1, 12, 12, 1, 1] 24
rigid atoms, others: [32, 1, 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])
total number of confs: 32
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037354 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037354
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037354/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037354
Building REAL300000037355
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037355'
/scratch/stefan/7769618/working/building/REAL300000037355 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037355

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037355/0 /scratch/stefan/7769618/working/building/REAL300000037355 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/377
`/scratch/stefan/7769618/working/3D/377' -> `0.mol2'
Preparing input files

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

`REAL300000037355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037355 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 12
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 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: REAL300000037355 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 33, 14, 15, 16, 17, 18, 19, 20, 21])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037355 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037355
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037355/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037355
Building REAL300000037356
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037356'
/scratch/stefan/7769618/working/building/REAL300000037356 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037356

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037356/0 /scratch/stefan/7769618/working/building/REAL300000037356 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/378
`/scratch/stefan/7769618/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000037356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037356 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 25, 25, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 56, 56, 6, 6, 6, 6, 53, 53, 1, 1, 1, 32, 32] 201
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037356 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 53, 53, 53, 26, 53, 53, 53, 134, 201, 201, 201, 26, 26, 26, 26, 1, 1, 53, 53, 53, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 703
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037356 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037356
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037356/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037356
Building REAL300000037357
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037357'
/scratch/stefan/7769618/working/building/REAL300000037357 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037357

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037357/0 /scratch/stefan/7769618/working/building/REAL300000037357 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/379
`/scratch/stefan/7769618/working/3D/379' -> `0.mol2'
Preparing input files

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

`REAL300000037357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037357 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 3, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 68, 37, 8, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 83, 83, 83, 68, 68, 68, 68, 68, 68, 37, 37, 37, 37, 1, 1, 83, 83] 83
rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037357 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 3, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 38, 38, 68, 68, 68, 68, 68, 68, 1, 1, 2, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 68, 68, 2, 2] 83
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])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037357 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037357
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037357/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037357
Building REAL300000037358
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037358'
/scratch/stefan/7769618/working/building/REAL300000037358 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037358

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037358/0 /scratch/stefan/7769618/working/building/REAL300000037358 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/380
`/scratch/stefan/7769618/working/3D/380' -> `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=CN=CC(Cl)=N1)

`REAL300000037358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037358 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 31, 31, 1, 1] 70
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037358 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 49, 50, 70, 70, 70, 70, 70, 70, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 70, 70] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037358 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037358/1 /scratch/stefan/7769618/working/building/REAL300000037358 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/381
`/scratch/stefan/7769618/working/3D/381' -> `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=CN=CC(Cl)=N1)

`REAL300000037358.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037358/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037358 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 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, 16, 16, 16, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 10, 4, 1, 1] 16
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037358 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 2, 2, 2, 1, 11, 16, 16, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037358 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037358
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037358/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037358/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037358
Building REAL300000037359
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037359'
/scratch/stefan/7769618/working/building/REAL300000037359 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037359

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037359/0 /scratch/stefan/7769618/working/building/REAL300000037359 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/382
`/scratch/stefan/7769618/working/3D/382' -> `0.mol2'
Preparing input files

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

`REAL300000037359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037359 none O=C([O-])C1=CC=CC(C=NNC2=CN=CC(Cl)=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 8, 4, 1, 1] 12
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24])
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: REAL300000037359 none O=C([O-])C1=CC=CC(C=NNC2=CN=CC(Cl)=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 5, 5, 11, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5, 11, 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, 26])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037359 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037359/1 /scratch/stefan/7769618/working/building/REAL300000037359 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/383
`/scratch/stefan/7769618/working/3D/383' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1Cl)

`REAL300000037359.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037359/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037359 none O=C([O-])C1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 114, 114, 114, 114, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 35, 35, 1, 1] 114
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24])
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: REAL300000037359 none O=C([O-])C1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 57, 58, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 8, 8, 114, 114] 114
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037359 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037359
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037359/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037359/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037359
Building REAL300000037360
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037360'
/scratch/stefan/7769618/working/building/REAL300000037360 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037360

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037360/0 /scratch/stefan/7769618/working/building/REAL300000037360 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/384
`/scratch/stefan/7769618/working/3D/384' -> `0.mol2'
Preparing input files

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

`REAL300000037360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037360 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14
rigid atoms, others: [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, 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: REAL300000037360 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 14
rigid atoms, others: [1, 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([0, 2, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 24
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037360 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037360
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037360/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037360
Building REAL300000037361
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037361'
/scratch/stefan/7769618/working/building/REAL300000037361 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037361

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037361/0 /scratch/stefan/7769618/working/building/REAL300000037361 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/385
`/scratch/stefan/7769618/working/3D/385' -> `0.mol2'
Preparing input files

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

`REAL300000037361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037361 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 46, 46, 46, 46, 46, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 201, 46, 46, 46, 16, 16, 1, 1, 46, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 612
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037361 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 3, 6, 19, 19, 19, 19, 19, 87, 195, 195, 201, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 87, 87, 201, 201, 19, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 36, 37, 38, 39, 40, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 455
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037361 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC(Cl)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 46, 46, 46, 46, 46, 46, 1, 18, 19, 19, 18, 19, 19, 18, 1, 1, 1, 7, 7, 46, 46, 1, 19, 19, 18, 19, 19] 201
rigid atoms, others: [35, 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, 34, 36, 37, 38, 39, 40])
total number of confs: 135
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037361 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037361
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037361/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037361
Building REAL300000037362
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037362'
/scratch/stefan/7769618/working/building/REAL300000037362 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037362

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037362/0 /scratch/stefan/7769618/working/building/REAL300000037362 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/386
`/scratch/stefan/7769618/working/3D/386' -> `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=CN=CC(Cl)=N1)

`REAL300000037362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037362 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [180, 180, 180, 120, 120, 120, 120, 120, 120, 120, 120, 120, 45, 8, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 120, 120, 120, 45, 45, 45, 45, 1, 1] 180
rigid atoms, others: [38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 356
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: REAL300000037362 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 56, 56, 120, 120, 120, 120, 120, 120, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 120, 120] 180
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])
total number of confs: 233
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037362 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037362
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037362/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037362
Building REAL300000037363
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037363'
/scratch/stefan/7769618/working/building/REAL300000037363 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037363

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037363/0 /scratch/stefan/7769618/working/building/REAL300000037363 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/387
`/scratch/stefan/7769618/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(N=NC1=CN=CC(Cl)=N1)CC2)

`REAL300000037363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037363 none O=C([O-])C1=CC=CC2=C1C(N=NC1=CN=CC(Cl)=N1)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1, 12, 12, 12, 12] 12
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30])
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: REAL300000037363 none O=C([O-])C1=CC=CC2=C1C(N=NC1=CN=CC(Cl)=N1)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 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/7769618/working/building/REAL300000037363 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037363/1 /scratch/stefan/7769618/working/building/REAL300000037363 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/388
`/scratch/stefan/7769618/working/3D/388' -> `1.mol2'
Preparing input files

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

`REAL300000037363.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037363/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037363 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CN=CC(Cl)=N1)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 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, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 1, 1, 4, 4, 4, 4] 4
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 8
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037363 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CN=CC(Cl)=N1)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 5, 5, 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, 4, 7, 7, 3, 7, 7, 7, 3, 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, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 4, 4, 1, 1, 1, 1] 4
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 27, 28, 29, 30] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037363 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037363
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037363/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037363/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037363
Building REAL300000037364
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037364'
/scratch/stefan/7769618/working/building/REAL300000037364 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037364

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037364/0 /scratch/stefan/7769618/working/building/REAL300000037364 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/389
`/scratch/stefan/7769618/working/3D/389' -> `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=CN=CC(Cl)=N3)C=C2)C=C1)

`REAL300000037364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037364 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 29, 29, 46, 46, 46, 46, 46, 46, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 46, 46, 1, 1, 3, 3] 75
rigid atoms, others: [34, 33, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037364 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 46, 75, 46, 75, 75, 46, 41, 46, 46, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 75, 75, 75, 75, 46, 46, 29, 29, 1, 1, 46, 46, 75, 75] 75
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 410
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037364 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 2, 11, 55, 55, 75, 75, 75, 75, 75, 75, 3, 3, 1, 1, 1, 1, 3, 3, 11, 11, 75, 75, 3, 3, 1, 1] 75
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037364 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037364
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037364/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037364
Building REAL300000037365
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037365'
/scratch/stefan/7769618/working/building/REAL300000037365 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037365

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037365/0 /scratch/stefan/7769618/working/building/REAL300000037365 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/390
`/scratch/stefan/7769618/working/3D/390' -> `0.mol2'
Preparing input files

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

`REAL300000037365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037365 none O=C([O-])C1=CC=C2NC=C(CN=NC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 32, 32, 1, 1, 87] 87
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 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: REAL300000037365 none O=C([O-])C1=CC=C2NC=C(CN=NC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 9, 9, 87, 87, 1] 87
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037365 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037365
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037365/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037365
Building REAL300000037366
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037366'
/scratch/stefan/7769618/working/building/REAL300000037366 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037366

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037366/0 /scratch/stefan/7769618/working/building/REAL300000037366 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/391
`/scratch/stefan/7769618/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CN=CC(Cl)=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037366 none COC1=CC(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 1, 12, 5, 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, 3, 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]
0  hydrogens 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, 119, 119, 119, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 118, 118, 195, 201, 201, 201, 201, 146, 146, 146, 119, 23, 23, 1, 1, 119, 201, 201, 201, 201] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37])
total number of confs: 402
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037366 none COC1=CC(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 1, 12, 5, 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, 3, 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]
0  hydrogens 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, 66, 66, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 4, 8, 8, 9, 9, 4, 4, 4, 1, 9, 9, 119, 119, 1, 8, 8, 8, 8] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037366 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037366/1 /scratch/stefan/7769618/working/building/REAL300000037366 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/392
`/scratch/stefan/7769618/working/3D/392' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CN=CC(Cl)=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037366.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037366/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037366 none COC1=CC(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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]
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: [61, 38, 38, 38, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 72, 95, 95, 104, 104, 61, 61, 61, 38, 14, 4, 1, 1, 38, 95, 95, 95, 95] 104
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37])
total number of confs: 303
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037366 none COC1=CC(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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]
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: [3, 1, 1, 1, 1, 1, 7, 7, 26, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 5, 12, 12, 20, 20, 4, 4, 4, 1, 7, 26, 38, 38, 1, 12, 12, 12, 12] 104
rigid atoms, others: [1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037366 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037366
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037366/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037366/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037366
Building REAL300000037367
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037367'
/scratch/stefan/7769618/working/building/REAL300000037367 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037367

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037367/0 /scratch/stefan/7769618/working/building/REAL300000037367 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/393
`/scratch/stefan/7769618/working/3D/393' -> `0.mol2'
Preparing input files

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

`REAL300000037367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037367 none O=C([O-])C1=C(Cl)SC(CN=NC2=CN=CC(Cl)=N2)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 195, 196, 195, 195, 195, 195, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 195, 46, 46, 1, 1, 195] 196
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 23])
total number of confs: 338
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037367 none O=C([O-])C1=C(Cl)SC(CN=NC2=CN=CC(Cl)=N2)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 78, 79, 196, 196, 196, 196, 196, 196, 1, 8, 8, 196, 196, 1] 196
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037367 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037367/1 /scratch/stefan/7769618/working/building/REAL300000037367 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/394
`/scratch/stefan/7769618/working/3D/394' -> `1.mol2'
Preparing input files

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

`REAL300000037367.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037367/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037367 none O=C([O-])C1=C(Cl)SC(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 10, 4, 1, 1, 21] 21
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 23])
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: REAL300000037367 none O=C([O-])C1=C(Cl)SC(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 1, 7, 21, 21, 21, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037367 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037367
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037367/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037367/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037367
Building REAL300000037368
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037368'
/scratch/stefan/7769618/working/building/REAL300000037368 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037368

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037368/0 /scratch/stefan/7769618/working/building/REAL300000037368 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/395
`/scratch/stefan/7769618/working/3D/395' -> `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=CN=CC(Cl)=N1)

`REAL300000037368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037368 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 29, 33, 35, 35, 35, 35, 29, 6, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 29, 29, 29, 29, 1, 1] 35
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037368 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 35, 35] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037368 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037368
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037368/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037368
Building REAL300000037369
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037369'
/scratch/stefan/7769618/working/building/REAL300000037369 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037369

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037369/0 /scratch/stefan/7769618/working/building/REAL300000037369 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/396
`/scratch/stefan/7769618/working/3D/396' -> `0.mol2'
Preparing input files

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

`REAL300000037369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037369 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 9, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 6, 2, 1, 1] 11
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23])
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: REAL300000037369 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 11, 11, 11, 11, 11, 11, 1, 1, 6, 10, 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, 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/7769618/working/building/REAL300000037369 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037369
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037369/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037369
Building REAL300000037370
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037370'
/scratch/stefan/7769618/working/building/REAL300000037370 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037370

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037370/0 /scratch/stefan/7769618/working/building/REAL300000037370 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/397
`/scratch/stefan/7769618/working/3D/397' -> `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=CN=CC(Cl)=N3)O2)=CC=C1O)

`REAL300000037370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037370 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 8, 69, 69, 122, 122, 122, 122, 122, 122, 1, 9, 9, 8, 8, 9, 1, 1, 8, 8, 122, 122, 9, 9, 18] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 228
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037370 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 122, 122, 122, 122, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 122, 122, 25, 25, 1, 1, 201, 201, 402] 402
rigid atoms, others: [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, 32, 33, 34])
total number of confs: 716
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037370 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 9, 9, 9, 49, 165, 165, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 9, 9, 49, 49, 201, 201, 1, 1, 2] 402
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037370 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037370
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037370/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037370
Building REAL300000037371
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037371'
/scratch/stefan/7769618/working/building/REAL300000037371 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037371

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037371/0 /scratch/stefan/7769618/working/building/REAL300000037371 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/398
`/scratch/stefan/7769618/working/3D/398' -> `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=CN=CC(Cl)=N1)

`REAL300000037371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037371 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 79, 79, 79, 79, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79, 36, 36, 1, 1] 79
rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 184
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037371 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 8, 47, 48, 79, 79, 79, 79, 79, 79, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 8, 79, 79] 79
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 151
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037371 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037371/1 /scratch/stefan/7769618/working/building/REAL300000037371 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/399
`/scratch/stefan/7769618/working/3D/399' -> `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=CN=CC(Cl)=N1)

`REAL300000037371.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037371/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037371 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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] 6
rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: REAL300000037371 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037371 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037371
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037371/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037371/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037371
Building REAL300000037372
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037372'
/scratch/stefan/7769618/working/building/REAL300000037372 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037372

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037372/0 /scratch/stefan/7769618/working/building/REAL300000037372 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/400
`/scratch/stefan/7769618/working/3D/400' -> `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=CN=CC(Cl)=N3)S2)C=C1)

`REAL300000037372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037372 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 3, 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: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 8, 66, 66, 113, 113, 113, 113, 113, 113, 1, 6, 6, 7, 7, 1, 1, 8, 8, 113, 113, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037372 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 3, 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, 113, 201, 113, 201, 201, 113, 113, 113, 113, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 113, 113, 31, 31, 1, 1, 201, 201] 201
rigid atoms, others: [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, 32, 33])
total number of confs: 859
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037372 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 39, 178, 178, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 8, 7, 39, 39, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037372 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037372
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037372/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037372
Building REAL300000037373
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037373'
/scratch/stefan/7769618/working/building/REAL300000037373 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037373

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037373/0 /scratch/stefan/7769618/working/building/REAL300000037373 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/401
`/scratch/stefan/7769618/working/3D/401' -> `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=CN=CC(Cl)=N3)S2)=C1)

`REAL300000037373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037373 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 9, 56, 56, 92, 92, 92, 92, 92, 92, 1, 12, 12, 12, 12, 1, 1, 9, 9, 92, 92, 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])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037373 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 92, 92, 19, 19, 1, 1, 201] 201
rigid atoms, others: [32, 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, 33])
total number of confs: 320
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037373 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 57, 186, 186, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 57, 57, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 378
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037373 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037373
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037373/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037373
Building REAL300000037374
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037374'
/scratch/stefan/7769618/working/building/REAL300000037374 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037374

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037374/0 /scratch/stefan/7769618/working/building/REAL300000037374 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/402
`/scratch/stefan/7769618/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(CN=NC2=CN=CC(Cl)=N2)S1)

`REAL300000037374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037374 none CCC1=CC(C(=O)[O-])=C(CN=NC2=CN=CC(Cl)=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 3, 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, 104, 104, 104, 104, 104, 116, 116, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 104, 42, 42, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 805
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037374 none CCC1=CC(C(=O)[O-])=C(CN=NC2=CN=CC(Cl)=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 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, 3, 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: [9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 49, 49, 104, 104, 104, 104, 104, 104, 1, 9, 9, 9, 9, 9, 1, 7, 7, 104, 104] 201
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037374 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037374/1 /scratch/stefan/7769618/working/building/REAL300000037374 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/403
`/scratch/stefan/7769618/working/3D/403' -> `1.mol2'
Preparing input files

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

`REAL300000037374.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037374/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037374 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CN=CC(Cl)=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 16, 16, 16, 16, 16, 16, 16, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 23, 23, 23, 23, 23, 16, 12, 4, 1, 1] 23
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037374 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CN=CC(Cl)=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 14, 16, 16, 16, 16, 16, 16, 1, 9, 9, 9, 8, 8, 1, 4, 14, 16, 16] 23
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037374 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037374
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037374/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037374/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037374
Building REAL300000037375
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037375'
/scratch/stefan/7769618/working/building/REAL300000037375 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037375

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037375/0 /scratch/stefan/7769618/working/building/REAL300000037375 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/404
`/scratch/stefan/7769618/working/3D/404' -> `0.mol2'
Preparing input files

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

`REAL300000037375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037375 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 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, 176, 176, 176, 176, 176, 176, 176, 176, 176, 64, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 176, 176, 176, 64, 64, 1, 1] 182
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 373
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037375 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 64, 65, 176, 176, 176, 176, 176, 176, 4, 4, 4, 1, 1, 1, 8, 8, 176, 176] 182
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037375 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037375/1 /scratch/stefan/7769618/working/building/REAL300000037375 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/405
`/scratch/stefan/7769618/working/3D/405' -> `1.mol2'
Preparing input files

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

`REAL300000037375.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037375/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037375 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 16, 4, 1, 1] 35
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 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: REAL300000037375 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 35, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 1, 10, 28, 35, 35] 35
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037375 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037375
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037375/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037375/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037375
Building REAL300000037376
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037376'
/scratch/stefan/7769618/working/building/REAL300000037376 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037376

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037376/0 /scratch/stefan/7769618/working/building/REAL300000037376 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/406
`/scratch/stefan/7769618/working/3D/406' -> `0.mol2'
Preparing input files

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

`REAL300000037376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037376 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 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, 9, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 8, 4, 1, 1, 9] 9
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 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: REAL300000037376 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 8, 9, 9, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037376 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037376/1 /scratch/stefan/7769618/working/building/REAL300000037376 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/407
`/scratch/stefan/7769618/working/3D/407' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(CN=NC3=CN=CC(Cl)=N3)C2=C1)

`REAL300000037376.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037376/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037376 none O=C([O-])C1=CC=C2SC=C(CN=NC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 77, 77, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 29, 29, 1, 1, 77] 77
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 29])
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: REAL300000037376 none O=C([O-])C1=CC=C2SC=C(CN=NC3=CN=CC(Cl)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 8, 8, 77, 77, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037376 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037376
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037376/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037376/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037376
Building REAL300000037377
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037377'
/scratch/stefan/7769618/working/building/REAL300000037377 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037377

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037377/0 /scratch/stefan/7769618/working/building/REAL300000037377 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/408
`/scratch/stefan/7769618/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(N=NC3=CN=CC(Cl)=N3)C2=C1)

`REAL300000037377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037377 none O=C([O-])C1=CN=C2CCCC(N=NC3=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 12] 12
rigid atoms, others: [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, 32])
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: REAL300000037377 none O=C([O-])C1=CN=C2CCCC(N=NC3=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32] set([12, 13, 14, 15, 16, 17, 18, 19, 30, 31])
total number of confs: 16
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037377 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037377/1 /scratch/stefan/7769618/working/building/REAL300000037377 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/409
`/scratch/stefan/7769618/working/3D/409' -> `1.mol2'
Preparing input files

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

`REAL300000037377.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037377/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037377 none O=C([O-])C1=CN=C2CCCC(=NNC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 5] 5
rigid atoms, others: [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, 32])
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: REAL300000037377 none O=C([O-])C1=CN=C2CCCC(=NNC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 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, 32] set([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/7769618/working/building/REAL300000037377 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037377
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037377/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037377/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037377
Building REAL300000037378
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037378'
/scratch/stefan/7769618/working/building/REAL300000037378 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037378

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037378/0 /scratch/stefan/7769618/working/building/REAL300000037378 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/410
`/scratch/stefan/7769618/working/3D/410' -> `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=CN=CC(Cl)=N2)=C1)

`REAL300000037378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037378 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 14, 4, 1, 1, 18] 18
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 26])
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: REAL300000037378 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 10, 10, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 10, 18, 18, 18, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037378 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037378/1 /scratch/stefan/7769618/working/building/REAL300000037378 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/411
`/scratch/stefan/7769618/working/3D/411' -> `1.mol2'
Preparing input files

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

`REAL300000037378.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037378/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037378 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 28, 28, 1, 1, 74] 74
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 26])
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: REAL300000037378 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 8, 46, 46, 74, 74, 74, 74, 74, 74, 1, 1, 1, 8, 8, 74, 74, 1] 74
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037378 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037378
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037378/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037378/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037378
Building REAL300000037379
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037379'
/scratch/stefan/7769618/working/building/REAL300000037379 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037379

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037379/0 /scratch/stefan/7769618/working/building/REAL300000037379 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/412
`/scratch/stefan/7769618/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CN=CC(Cl)=N2)=CC=C1C(=O)[O-])

`REAL300000037379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037379 none COC1=CC(CN=NC2=CN=CC(Cl)=N2)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 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: [201, 113, 113, 113, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 180, 180, 201, 201, 201, 113, 23, 23, 1, 1, 113, 113] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 624
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037379 none COC1=CC(CN=NC2=CN=CC(Cl)=N2)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 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, 8, 66, 66, 113, 113, 113, 113, 113, 113, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 8, 8, 113, 113, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037379 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037379
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037379/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037379
Building REAL300000037380
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037380'
/scratch/stefan/7769618/working/building/REAL300000037380 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037380

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037380/0 /scratch/stefan/7769618/working/building/REAL300000037380 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/413
`/scratch/stefan/7769618/working/3D/413' -> `0.mol2'
Preparing input files

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

`REAL300000037380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037380 none O=C([O-])C1=CC(F)=C(C=NNC2=CN=CC(Cl)=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 2, 1, 1, 6] 6
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 26])
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: REAL300000037380 none O=C([O-])C1=CC(F)=C(C=NNC2=CN=CC(Cl)=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 5, 6, 6, 1] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037380 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037380
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037380/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037380
Building REAL300000037381
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037381'
/scratch/stefan/7769618/working/building/REAL300000037381 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037381

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037381/0 /scratch/stefan/7769618/working/building/REAL300000037381 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/414
`/scratch/stefan/7769618/working/3D/414' -> `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=CN=CC(Cl)=N2)=C1)

`REAL300000037381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037381 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 16, 8, 1, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 28, 10, 4, 1, 1, 14] 28
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 27])
total number of confs: 51
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037381 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 16, 8, 1, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 9, 14, 14, 14, 1] 28
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: 37
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037381 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037381/1 /scratch/stefan/7769618/working/building/REAL300000037381 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/415
`/scratch/stefan/7769618/working/3D/415' -> `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=CN=CC(Cl)=N2)=C1)

`REAL300000037381.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037381/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037381 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 6] 6
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 26])
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: REAL300000037381 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037381 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037381
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037381/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037381/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037381
Building REAL300000037382
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037382'
/scratch/stefan/7769618/working/building/REAL300000037382 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037382

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037382/0 /scratch/stefan/7769618/working/building/REAL300000037382 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/416
`/scratch/stefan/7769618/working/3D/416' -> `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=CN=CC(Cl)=N3)C=C2)O1)

`REAL300000037382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037382 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 101, 101, 101, 101, 101, 101, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 8, 101, 101, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037382 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 200, 200, 101, 101, 98, 25, 101, 101, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 200, 200, 200, 101, 101, 101, 101, 22, 22, 1, 1, 101, 101] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 548
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037382 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 35, 176, 177, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 5, 5, 5, 5, 35, 35, 201, 201, 5, 5] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 347
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037382 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037382
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037382/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037382
Building REAL300000037383
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037383'
/scratch/stefan/7769618/working/building/REAL300000037383 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037383

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037383/0 /scratch/stefan/7769618/working/building/REAL300000037383 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/417
`/scratch/stefan/7769618/working/3D/417' -> `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=CN=CC(Cl)=N2)=C1O)

`REAL300000037383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037383 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CN=CC(Cl)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 11, 4, 1, 1, 42] 42
rigid atoms, others: [32, 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, 33])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037383 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CN=CC(Cl)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 17, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 11, 17, 21, 21, 2] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037383 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037383/1 /scratch/stefan/7769618/working/building/REAL300000037383 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/418
`/scratch/stefan/7769618/working/3D/418' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CN=CC(Cl)=N2)=C1O)

`REAL300000037383.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037383/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037383 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CN=CC(Cl)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 33, 33, 1, 1, 170] 170
rigid atoms, others: [32, 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, 33])
total number of confs: 346
number of broken/clashed sets: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037383 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CN=CC(Cl)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 8, 8, 85, 85, 2] 170
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 148
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037383 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037383
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037383/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037383/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037383
Building REAL300000037384
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037384'
/scratch/stefan/7769618/working/building/REAL300000037384 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037384

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037384/0 /scratch/stefan/7769618/working/building/REAL300000037384 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/419
`/scratch/stefan/7769618/working/3D/419' -> `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=CN=CC(Cl)=N3)C=C2)=C1)

`REAL300000037384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037384 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 56, 56, 103, 103, 103, 103, 103, 103, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 103, 103, 1, 1, 3] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037384 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 164, 164, 158, 164, 164, 103, 40, 103, 103, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 164, 201, 201, 164, 164, 164, 103, 103, 22, 22, 1, 1, 103, 103, 164] 201
rigid atoms, others: [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, 34, 37, 38, 39])
total number of confs: 752
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037384 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC(Cl)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 17, 110, 110, 164, 164, 164, 164, 164, 164, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 17, 17, 164, 164, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037384 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037384
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037384/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037384
Building REAL300000037385
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037385'
/scratch/stefan/7769618/working/building/REAL300000037385 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037385

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037385/0 /scratch/stefan/7769618/working/building/REAL300000037385 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/420
`/scratch/stefan/7769618/working/3D/420' -> `0.mol2'
Preparing input files

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

`REAL300000037385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037385 none O=C([O-])C1=C(C=NNC2=CN=CC(Cl)=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 16, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 6, 2, 1, 1, 8] 8
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 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: REAL300000037385 none O=C([O-])C1=C(C=NNC2=CN=CC(Cl)=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 16, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 7, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 7, 8, 8, 1] 8
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037385 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037385/1 /scratch/stefan/7769618/working/building/REAL300000037385 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/421
`/scratch/stefan/7769618/working/3D/421' -> `1.mol2'
Preparing input files

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

`REAL300000037385.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037385/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037385 none O=C([O-])C1=C(CN=NC2=CN=CC(Cl)=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 16, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 34, 34, 1, 1, 111] 111
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 23])
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: REAL300000037385 none O=C([O-])C1=C(CN=NC2=CN=CC(Cl)=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 16, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 3, 1, 1, 1, 8, 56, 56, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 8, 8, 111, 111, 1] 111
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037385 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037385
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037385/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037385/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037385
Building REAL300000037386
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037386'
/scratch/stefan/7769618/working/building/REAL300000037386 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037386

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037386/0 /scratch/stefan/7769618/working/building/REAL300000037386 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/422
`/scratch/stefan/7769618/working/3D/422' -> `0.mol2'
Preparing input files

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

`REAL300000037386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037386 none CCOC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 95, 55, 55, 55, 14, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 169, 200, 201, 201, 97, 97, 97, 97, 97, 55, 14, 14, 1, 1, 55, 55, 200, 200] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37])
total number of confs: 535
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037386 none CCOC1=CC(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 42, 42, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 7, 19, 23, 23, 5, 5, 5, 5, 5, 1, 6, 6, 55, 55, 1, 1, 19, 19] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 34, 16, 17, 18, 35, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37])
total number of confs: 177
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037386 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037386
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037386/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037386
Building REAL300000037387
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037387'
/scratch/stefan/7769618/working/building/REAL300000037387 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037387

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037387/0 /scratch/stefan/7769618/working/building/REAL300000037387 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/423
`/scratch/stefan/7769618/working/3D/423' -> `0.mol2'
Preparing input files

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

`REAL300000037387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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: [13, 10, 13, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 30, 30, 30] 30
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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: [13, 12, 13, 12, 12, 12, 12, 30, 30, 30, 30, 30, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 8, 2, 1, 1] 30
rigid atoms, others: [36, 37, 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: 70
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 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] 30
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037387 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037387/1 /scratch/stefan/7769618/working/building/REAL300000037387 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/424
`/scratch/stefan/7769618/working/3D/424' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC(Cl)=N1)

`REAL300000037387.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037387/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 57, 164, 164, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 57, 57, 201, 201] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 71, 89, 71, 71, 71, 71, 201, 201, 201, 201, 201, 71, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 24, 24, 1, 1] 201
rigid atoms, others: [36, 37, 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: 570
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037387 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 13, 1, 1, 1, 8, 46, 46, 71, 71, 71, 71, 71, 71, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 8, 8, 71, 71] 201
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037387 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037387
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037387/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037387/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037387
Building REAL300000037388
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037388'
/scratch/stefan/7769618/working/building/REAL300000037388 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037388

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037388/0 /scratch/stefan/7769618/working/building/REAL300000037388 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/425
`/scratch/stefan/7769618/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(CN=NC2=CN=CC(Cl)=N2)=C1C(=O)[O-])

`REAL300000037388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037388 none COC1=CC=C(C)C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 48, 48, 48, 48, 48, 48, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 72, 72, 72, 48, 48, 48, 48, 48, 28, 28, 1, 1] 72
rigid atoms, others: [32, 33, 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: 165
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037388 none COC1=CC=C(C)C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 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, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 48, 48, 48, 48, 48, 48, 1, 1, 2, 2, 4, 4, 4, 1, 1, 2, 2, 2, 7, 7, 48, 48] 72
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 93
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037388 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037388/1 /scratch/stefan/7769618/working/building/REAL300000037388 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/426
`/scratch/stefan/7769618/working/3D/426' -> `1.mol2'
Preparing input files

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

`REAL300000037388.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037388/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037388 none COC1=CC=C(C)C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 23, 23, 23, 23, 23, 23, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 14, 4, 1, 1] 29
rigid atoms, others: [32, 33, 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: 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: REAL300000037388 none COC1=CC=C(C)C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
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, 1, 1, 1, 7, 7, 19, 23, 23, 23, 23, 23, 23, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 7, 19, 23, 23] 29
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037388 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037388
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037388/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037388/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037388
Building REAL300000037389
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037389'
/scratch/stefan/7769618/working/building/REAL300000037389 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037389

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037389/0 /scratch/stefan/7769618/working/building/REAL300000037389 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/427
`/scratch/stefan/7769618/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC(Cl)=N2)=C1C(=O)[O-])

`REAL300000037389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037389 none CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 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, 3, 7, 7, 2, 2, 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, 96, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 32, 32, 1, 1] 96
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037389 none CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 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, 3, 7, 7, 2, 2, 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, 1, 7, 53, 53, 96, 96, 96, 96, 96, 96, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 7, 7, 96, 96] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037389 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037389/1 /scratch/stefan/7769618/working/building/REAL300000037389 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/428
`/scratch/stefan/7769618/working/3D/428' -> `1.mol2'
Preparing input files

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

`REAL300000037389.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037389/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037389 none CN1C2=CC=C(F)C=C2C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 1, 1] 9
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300000037389 none CN1C2=CC=C(F)C=C2C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 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, 4, 4, 8, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037389 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037389
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037389/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037389/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037389
Building REAL300000037390
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037390'
/scratch/stefan/7769618/working/building/REAL300000037390 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037390

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037390/0 /scratch/stefan/7769618/working/building/REAL300000037390 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/429
`/scratch/stefan/7769618/working/3D/429' -> `0.mol2'
Preparing input files

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

`REAL300000037390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037390 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 45, 45, 79, 79, 79, 79, 79, 79, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 79, 79, 1, 1, 1, 1] 79
rigid atoms, others: [32, 1, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28])
total number of confs: 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: REAL300000037390 none CC(N=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 36, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 36, 36, 36, 36, 1, 1, 79, 79, 79, 79] 79
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037390 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037390
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037390/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037390
Building REAL300000037391
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037391'
/scratch/stefan/7769618/working/building/REAL300000037391 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037391

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037391/0 /scratch/stefan/7769618/working/building/REAL300000037391 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/430
`/scratch/stefan/7769618/working/3D/430' -> `0.mol2'
Preparing input files

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

`REAL300000037391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037391 none O=C([O-])C1=C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 17, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 6, 2, 1, 1, 8] 8
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 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: REAL300000037391 none O=C([O-])C1=C(C=NNC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 17, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 7, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 7, 8, 8, 1] 8
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037391 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037391/1 /scratch/stefan/7769618/working/building/REAL300000037391 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/431
`/scratch/stefan/7769618/working/3D/431' -> `1.mol2'
Preparing input files

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

`REAL300000037391.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037391/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037391 none O=C([O-])C1=C(CN=NC2=CN=CC(Cl)=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 34, 34, 1, 1, 111] 111
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 23])
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: REAL300000037391 none O=C([O-])C1=C(CN=NC2=CN=CC(Cl)=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 3, 1, 1, 1, 8, 56, 56, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 8, 8, 111, 111, 1] 111
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037391 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037391
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037391/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037391/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037391
Building REAL300000037392
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037392'
/scratch/stefan/7769618/working/building/REAL300000037392 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037392

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037392/0 /scratch/stefan/7769618/working/building/REAL300000037392 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/432
`/scratch/stefan/7769618/working/3D/432' -> `0.mol2'
Preparing input files

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

`REAL300000037392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037392 none O=C([O-])C1=C2NC=C(CN=NC3=CN=CC(Cl)=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 6, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 36, 36, 1, 1, 118, 118, 118] 118
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30])
total number of confs: 221
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037392 none O=C([O-])C1=C2NC=C(CN=NC3=CN=CC(Cl)=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 1, 6, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 73, 74, 118, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 9, 9, 118, 118, 1, 1, 1] 118
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037392 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037392
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037392/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037392
Building REAL300000037393
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037393'
/scratch/stefan/7769618/working/building/REAL300000037393 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037393

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037393/0 /scratch/stefan/7769618/working/building/REAL300000037393 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/433
`/scratch/stefan/7769618/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC(Cl)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037393 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
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: [6, 1, 6, 25, 25, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 34, 34, 1, 1, 1, 1, 1] 34
rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29])
total number of confs: 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: REAL300000037393 none CC(N=NC1=CN=CC(Cl)=N1)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', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
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: [28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 28, 28, 28, 28, 1, 1, 34, 34, 34, 34, 34] 34
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037393 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037393
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037393/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037393
Building REAL300000037394
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037394'
/scratch/stefan/7769618/working/building/REAL300000037394 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037394

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037394/0 /scratch/stefan/7769618/working/building/REAL300000037394 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/434
`/scratch/stefan/7769618/working/3D/434' -> `0.mol2'
Preparing input files

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

`REAL300000037394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037394 none O=C([O-])C1=CC2=CC(CN=NC3=CN=CC(Cl)=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 32, 32, 1, 1, 91, 91] 91
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29])
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: REAL300000037394 none O=C([O-])C1=CC2=CC(CN=NC3=CN=CC(Cl)=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 66, 66, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 8, 8, 91, 91, 1, 1] 91
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037394 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037394
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037394/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037394
Building REAL300000037395
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037395'
/scratch/stefan/7769618/working/building/REAL300000037395 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037395

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037395/0 /scratch/stefan/7769618/working/building/REAL300000037395 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/435
`/scratch/stefan/7769618/working/3D/435' -> `0.mol2'
Preparing input files

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

`REAL300000037395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037395 none O=C([O-])C1=CN=C2C(C=NNC3=CN=CC(Cl)=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 8, 4, 1, 1, 9, 9, 9] 10
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 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: REAL300000037395 none O=C([O-])C1=CN=C2C(C=NNC3=CN=CC(Cl)=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 8, 9, 9, 1, 1, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037395 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037395/1 /scratch/stefan/7769618/working/building/REAL300000037395 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/436
`/scratch/stefan/7769618/working/3D/436' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(CN=NC3=CN=CC(Cl)=N3)=CC=CN12)

`REAL300000037395.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037395/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037395 none O=C([O-])C1=CN=C2C(CN=NC3=CN=CC(Cl)=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 28, 28, 1, 1, 80, 80, 80] 80
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037395 none O=C([O-])C1=CN=C2C(CN=NC3=CN=CC(Cl)=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 9, 9, 80, 80, 1, 1, 1] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037395 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037395
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037395/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037395/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037395
Building REAL300000037396
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037396'
/scratch/stefan/7769618/working/building/REAL300000037396 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037396

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037396/0 /scratch/stefan/7769618/working/building/REAL300000037396 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/437
`/scratch/stefan/7769618/working/3D/437' -> `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=CN=CC(Cl)=N2)O1)

`REAL300000037396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037396 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC(Cl)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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: [56, 56, 56, 56, 56, 56, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 34, 72, 72, 72, 72, 72, 72, 56, 56, 56, 20, 20, 1, 1, 1, 1, 7, 7, 72, 72] 135
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037396 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC(Cl)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 135, 135, 135, 120, 93, 72, 72, 72, 72, 72, 72, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 120, 120, 72, 72, 72, 72, 36, 36, 1, 1] 135
rigid atoms, others: [36, 37, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 383
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037396 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC(Cl)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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, 8, 38, 56, 56, 38, 56, 56, 56, 70, 119, 119, 135, 135, 135, 135, 135, 135, 1, 1, 1, 8, 8, 56, 56, 38, 56, 70, 70, 135, 135] 135
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037396 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037396
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037396/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037396
Building REAL300000037397
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037397'
/scratch/stefan/7769618/working/building/REAL300000037397 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037397

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037397/0 /scratch/stefan/7769618/working/building/REAL300000037397 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/438
`/scratch/stefan/7769618/working/3D/438' -> `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=CN=CC(Cl)=N1)

`REAL300000037397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037397 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 6, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 2, 1, 1] 7
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24])
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: REAL300000037397 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 1, 1, 4, 4, 6, 7, 7, 7, 7, 7, 7, 1, 1, 1, 4, 6, 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])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037397 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037397/1 /scratch/stefan/7769618/working/building/REAL300000037397 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/439
`/scratch/stefan/7769618/working/3D/439' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC(Cl)=N1)

`REAL300000037397.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037397/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037397 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 61, 61, 61, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 27, 27, 1, 1] 61
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24])
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: REAL300000037397 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 49, 50, 61, 61, 61, 61, 61, 61, 1, 1, 1, 8, 8, 61, 61] 61
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037397 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037397
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037397/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037397/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037397
Building REAL300000037398
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037398'
/scratch/stefan/7769618/working/building/REAL300000037398 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037398

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037398/0 /scratch/stefan/7769618/working/building/REAL300000037398 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/440
`/scratch/stefan/7769618/working/3D/440' -> `0.mol2'
Preparing input files

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

`REAL300000037398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037398 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 108, 108, 108, 108, 108, 151, 108, 108, 108, 108, 108, 108, 147, 147, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 108, 151, 151, 151, 108, 108, 47, 47, 1, 1] 201
rigid atoms, others: [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, 36])
total number of confs: 583
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037398 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 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, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 46, 46, 108, 108, 108, 108, 108, 108, 3, 3, 3, 1, 4, 4, 4, 1, 1, 6, 6, 108, 108] 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])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037398 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037398
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037398/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037398
Building REAL300000037399
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037399'
/scratch/stefan/7769618/working/building/REAL300000037399 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037399

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037399/0 /scratch/stefan/7769618/working/building/REAL300000037399 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/441
`/scratch/stefan/7769618/working/3D/441' -> `0.mol2'
Preparing input files

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

`REAL300000037399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037399 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 6, 2, 1, 1] 11
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 28, 29] 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: 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: REAL300000037399 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 6, 11, 11, 11] 11
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])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037399 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037399/1 /scratch/stefan/7769618/working/building/REAL300000037399 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/442
`/scratch/stefan/7769618/working/3D/442' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=CN=CC(Cl)=N1)

`REAL300000037399.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037399/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037399 none O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 34, 34, 1, 1] 70
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 28, 29] 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: 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: REAL300000037399 none O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 8, 8, 70, 70] 70
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])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037399 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037399
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037399/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037399/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037399
Building REAL300000037400
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037400'
/scratch/stefan/7769618/working/building/REAL300000037400 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037400

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037400/0 /scratch/stefan/7769618/working/building/REAL300000037400 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/443
`/scratch/stefan/7769618/working/3D/443' -> `0.mol2'
Preparing input files

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

`REAL300000037400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037400 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 6, 2, 1, 1, 11] 11
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 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: REAL300000037400 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 3, 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, 3, 3, 1, 1, 6, 6, 10, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 10, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 20, 21, 22, 27] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037400 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037400/1 /scratch/stefan/7769618/working/building/REAL300000037400 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/444
`/scratch/stefan/7769618/working/3D/444' -> `1.mol2'
Preparing input files

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

`REAL300000037400.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037400/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037400 none N#CC1=CC=C(C(=O)[O-])C(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 34, 34, 1, 1, 74] 74
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 27])
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: REAL300000037400 none N#CC1=CC=C(C(=O)[O-])C(CN=NC2=CN=CC(Cl)=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 54, 54, 74, 74, 74, 74, 74, 74, 1, 1, 1, 8, 8, 74, 74, 1] 74
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 20, 21, 22, 27] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037400 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037400
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037400/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037400/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037400
Building REAL300000037401
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037401'
/scratch/stefan/7769618/working/building/REAL300000037401 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037401

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037401/0 /scratch/stefan/7769618/working/building/REAL300000037401 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/445
`/scratch/stefan/7769618/working/3D/445' -> `0.mol2'
Preparing input files

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

`REAL300000037401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037401 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 197, 84, 84, 85, 85, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 201, 201, 85, 85, 18, 18, 1, 1, 85] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 337
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037401 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [24, 19, 24, 7, 1, 1, 1, 1, 1, 1, 7, 47, 47, 85, 85, 85, 85, 85, 85, 1, 1, 1, 19, 19, 1, 1, 7, 7, 85, 85, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037401 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037401
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037401/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037401
Building REAL300000037402
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037402'
/scratch/stefan/7769618/working/building/REAL300000037402 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037402

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037402/0 /scratch/stefan/7769618/working/building/REAL300000037402 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/446
`/scratch/stefan/7769618/working/3D/446' -> `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=CN=CC(Cl)=N2)C=C1)

`REAL300000037402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037402 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 6, 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, 3, 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, 119, 27, 119, 119, 27, 118, 118, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 118, 118, 27, 27, 1, 1, 118, 118] 201
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 980
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037402 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CN=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 1, 7, 7, 6, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 61, 61, 118, 118, 118, 118, 118, 118, 1, 1, 9, 9, 5, 1, 1, 8, 8, 118, 118, 1, 1] 201
rigid atoms, others: [33, 34, 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])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037402 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037402
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037402/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037402
Building REAL300000037403
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037403'
/scratch/stefan/7769618/working/building/REAL300000037403 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037403

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037403/0 /scratch/stefan/7769618/working/building/REAL300000037403 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/447
`/scratch/stefan/7769618/working/3D/447' -> `0.mol2'
Preparing input files

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

`REAL300000037403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037403 none O=C([O-])C1=CC2=C(C=NNC3=CN=CC(Cl)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 6, 4, 1, 1, 10, 10] 10
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037403 none O=C([O-])C1=CC2=C(C=NNC3=CN=CC(Cl)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 9, 9, 9, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 10, 1, 1] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037403 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037403/1 /scratch/stefan/7769618/working/building/REAL300000037403 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/448
`/scratch/stefan/7769618/working/3D/448' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(CN=NC3=CN=CC(Cl)=N3)C(F)=CC=C2S1)

`REAL300000037403.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037403/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037403 none O=C([O-])C1=CC2=C(CN=NC3=CN=CC(Cl)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 29, 29, 1, 1, 69, 69] 69
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29])
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: REAL300000037403 none O=C([O-])C1=CC2=C(CN=NC3=CN=CC(Cl)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 48, 48, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 7, 7, 69, 69, 1, 1] 69
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037403 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037403
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037403/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037403/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037403
Building REAL300000037404
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037404'
/scratch/stefan/7769618/working/building/REAL300000037404 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037404

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037404/0 /scratch/stefan/7769618/working/building/REAL300000037404 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/449
`/scratch/stefan/7769618/working/3D/449' -> `0.mol2'
Preparing input files

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

`REAL300000037404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037404 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 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, 163, 163, 163, 152, 163, 163, 163, 163, 163, 62, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 163, 163, 163, 62, 62, 1, 1] 167
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 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: REAL300000037404 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CN=CC(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', '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, 8, 1, 1, 16, 8, 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, 3, 7, 7, 7, 3, 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, 2, 2, 1, 1, 1, 1, 8, 61, 62, 163, 163, 163, 163, 163, 163, 4, 4, 4, 1, 1, 1, 8, 8, 163, 163] 167
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 24, 25, 26] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037404 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037404
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037404/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037404
Building REAL300000037405
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037405'
/scratch/stefan/7769618/working/building/REAL300000037405 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037405

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037405/0 /scratch/stefan/7769618/working/building/REAL300000037405 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/450
`/scratch/stefan/7769618/working/3D/450' -> `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=CN=CC(Cl)=N3)=N2)C1)

`REAL300000037405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037405 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [17, 9, 17, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 9, 50, 50, 70, 70, 70, 70, 70, 70, 1, 9, 9, 9, 1, 1, 9, 9, 70, 70, 9, 9] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037405 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 70, 201, 70, 70, 70, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 70, 70, 18, 18, 1, 1, 201, 201] 201
rigid atoms, others: [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, 32, 33])
total number of confs: 491
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037405 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CN=CC(Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 16, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 38, 172, 172, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 9, 9, 38, 38, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037405 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037405
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037405/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037405
Building REAL300000037406
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037406'
/scratch/stefan/7769618/working/building/REAL300000037406 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037406

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037406/0 /scratch/stefan/7769618/working/building/REAL300000037406 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/451
`/scratch/stefan/7769618/working/3D/451' -> `0.mol2'
Preparing input files

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

`REAL300000037406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037406 none CC(N=NC1=NC=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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]
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, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 1, 1, 3, 3, 3, 3, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 12
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 45, 46, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300000037406 none CC(N=NC1=NC=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 11, 18, 18, 11, 11, 71, 71, 71, 149, 149, 179, 179, 201, 201, 201, 18, 18, 11, 11, 11, 11, 1, 1, 1, 18, 18, 149, 149, 149, 179, 179, 179, 179, 201, 201, 18, 18] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 820
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037406 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037406
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037406/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037406
Building REAL300000037407
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037407'
/scratch/stefan/7769618/working/building/REAL300000037407 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037407

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037407/0 /scratch/stefan/7769618/working/building/REAL300000037407 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/452
`/scratch/stefan/7769618/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000037407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037407 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 47, 47, 88, 88, 47, 88, 88, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 7, 88, 47, 88, 1, 1, 12, 12, 1, 1] 114
rigid atoms, others: [32, 1, 35, 36, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037407 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [16, 1, 18, 93, 93, 114, 114, 96, 114, 114, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 16, 16, 17, 19, 114, 101, 114, 12, 12, 1, 1, 12, 12] 114
rigid atoms, others: [34, 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, 32, 35, 36])
total number of confs: 283
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037407 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 50, 90, 90, 61, 61, 114, 114, 114, 114, 114, 114, 114, 90, 90, 50, 50, 50, 50, 1, 1, 1, 90, 90, 114, 114, 90, 90] 114
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 1, 2, 10, 11, 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: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037407 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037407
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037407/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037407
Building REAL300000037408
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037408'
/scratch/stefan/7769618/working/building/REAL300000037408 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037408

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037408/0 /scratch/stefan/7769618/working/building/REAL300000037408 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/453
`/scratch/stefan/7769618/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=N2)=CC=C1OCC(=O)[O-])

`REAL300000037408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037408 none COC1=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [90, 66, 66, 66, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 160, 201, 201, 201, 90, 90, 90, 66, 20, 20, 1, 1, 1, 66, 66, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 531
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037408 none COC1=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 36, 36, 71, 71, 37, 71, 71, 1, 1, 1, 1, 9, 19, 30, 30, 3, 3, 3, 1, 6, 6, 71, 37, 71, 1, 1, 19, 19] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 14, 15, 16, 17, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037408 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037408
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037408/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037408
Building REAL300000037409
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037409'
/scratch/stefan/7769618/working/building/REAL300000037409 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037409

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037409/0 /scratch/stefan/7769618/working/building/REAL300000037409 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/454
`/scratch/stefan/7769618/working/3D/454' -> `0.mol2'
Preparing input files

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

`REAL300000037409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037409 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 24, 24, 63, 63, 24, 63, 63, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 20, 1, 1, 5, 5, 5, 5, 63, 24, 63, 1, 1, 9, 17, 17, 1, 1] 126
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037409 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 35, 64, 64, 53, 53, 92, 92, 92, 121, 124, 124, 124, 64, 64, 35, 35, 35, 35, 1, 1, 1, 64, 64, 121, 124, 124, 64, 64] 124
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 1, 2, 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])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037409 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037409
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037409/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037409
Building REAL300000037410
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037410'
/scratch/stefan/7769618/working/building/REAL300000037410 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037410

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037410/0 /scratch/stefan/7769618/working/building/REAL300000037410 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/455
`/scratch/stefan/7769618/working/3D/455' -> `0.mol2'
Preparing input files

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

`REAL300000037410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037410 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 18, 18, 29, 29, 18, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 5, 29, 18, 29, 1, 1, 9, 9, 9, 9, 9, 1, 1] 61
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037410 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 14, 19, 19, 14, 14, 29, 29, 29, 47, 47, 47, 47, 47, 19, 19, 14, 14, 14, 14, 1, 1, 1, 19, 19, 47, 47, 47, 47, 47, 19, 19] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037410 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037410
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037410/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037410
Building REAL300000037411
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037411'
/scratch/stefan/7769618/working/building/REAL300000037411 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037411

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037411/0 /scratch/stefan/7769618/working/building/REAL300000037411 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/456
`/scratch/stefan/7769618/working/3D/456' -> `0.mol2'
Preparing input files

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

`REAL300000037411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037411 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 6, 6, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 7, 6, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 21
rigid atoms, others: [1, 34, 43, 33, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
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: REAL300000037411 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 4, 4] 12
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037411 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037411
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037411/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037411
Building REAL300000037412
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037412'
/scratch/stefan/7769618/working/building/REAL300000037412 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037412

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037412/0 /scratch/stefan/7769618/working/building/REAL300000037412 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/457
`/scratch/stefan/7769618/working/3D/457' -> `0.mol2'
Preparing input files

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

`REAL300000037412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037412 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 31, 31, 69, 69, 31, 69, 69, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 16, 16, 1, 1, 7, 7, 7, 7, 69, 31, 69, 1, 1, 8, 13, 13, 13, 1, 1] 101
rigid atoms, others: [1, 34, 33, 40, 10, 11, 12, 13, 14, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037412 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 4, 7, 7, 7, 8, 8, 8, 8, 8, 8, 6, 6, 4, 4, 4, 4, 1, 1, 1, 6, 6, 8, 8, 8, 8, 6, 6] 8
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037412 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037412
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037412/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037412
Building REAL300000037413
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037413'
/scratch/stefan/7769618/working/building/REAL300000037413 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037413

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037413/0 /scratch/stefan/7769618/working/building/REAL300000037413 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/458
`/scratch/stefan/7769618/working/3D/458' -> `0.mol2'
Preparing input files

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

`REAL300000037413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037413 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 161, 104, 104, 104, 74, 104, 104, 104, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 104, 103, 104, 49, 49, 1, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 681
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: REAL300000037413 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 28, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 35, 36, 88, 84, 36, 88, 88, 28, 28, 1, 1, 1, 6, 6, 88, 36, 88] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 428
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037413 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037413
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037413/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037413
Building REAL300000037414
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037414'
/scratch/stefan/7769618/working/building/REAL300000037414 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037414

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037414/0 /scratch/stefan/7769618/working/building/REAL300000037414 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/459
`/scratch/stefan/7769618/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=N2)=C1)

`REAL300000037414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037414 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=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', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 15, 12, 12, 12, 12, 12, 6, 2, 1, 1, 1, 1, 1, 1, 1, 7, 43, 44, 70, 64, 44, 70, 70, 1, 12, 12, 12, 12, 6, 6, 1, 1, 1, 7, 7, 70, 44, 70, 1] 201
rigid atoms, others: [32, 33, 34, 40, 10, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 235
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037414 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=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', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 120, 96, 72, 72, 72, 72, 72, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 119, 119, 72, 72, 72, 24, 24, 1, 1, 1, 72] 201
rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40])
total number of confs: 419
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037414 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=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', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 7, 12, 12, 7, 12, 12, 55, 186, 187, 201, 179, 187, 201, 201, 12, 1, 1, 1, 1, 5, 5, 12, 12, 12, 55, 55, 201, 187, 201, 12] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 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: 535
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037414 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037414
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037414/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037414
Building REAL300000037415
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037415'
/scratch/stefan/7769618/working/building/REAL300000037415 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037415

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037415/0 /scratch/stefan/7769618/working/building/REAL300000037415 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/460
`/scratch/stefan/7769618/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1[N+](=O)[O-])

`REAL300000037415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037415 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 142, 42, 26, 78, 78, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 79, 79, 201, 201, 78, 78, 26, 26, 1, 1, 1, 78] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 727
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: REAL300000037415 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 18, 20, 7, 1, 1, 1, 1, 1, 1, 7, 49, 49, 114, 108, 49, 114, 114, 1, 1, 1, 2, 2, 18, 18, 1, 1, 7, 7, 114, 50, 114, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 396
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037415 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037415
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037415/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037415
Building REAL300000037416
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037416'
/scratch/stefan/7769618/working/building/REAL300000037416 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037416

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037416/0 /scratch/stefan/7769618/working/building/REAL300000037416 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/461
`/scratch/stefan/7769618/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=N3)C=C2)=C1)

`REAL300000037416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037416 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 56, 56, 119, 115, 56, 119, 119, 1, 1, 8, 8, 8, 8, 1, 1, 1, 1, 9, 9, 119, 56, 119, 1, 1, 8] 201
rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 39, 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, 40])
total number of confs: 357
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037416 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 83, 76, 50, 25, 76, 76, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 83, 83, 76, 76, 25, 25, 1, 1, 1, 76, 76, 201] 201
rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 533
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037416 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 8, 43, 162, 162, 201, 194, 162, 201, 201, 8, 8, 1, 2, 2, 2, 8, 8, 8, 8, 43, 43, 201, 162, 201, 7, 8, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 40, 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])
total number of confs: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037416 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037416
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037416/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037416
Building REAL300000037417
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037417'
/scratch/stefan/7769618/working/building/REAL300000037417 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037417

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037417/0 /scratch/stefan/7769618/working/building/REAL300000037417 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/462
`/scratch/stefan/7769618/working/3D/462' -> `0.mol2'
Preparing input files

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

`REAL300000037417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037417 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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: [11, 11, 11, 11, 10, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 45, 45, 38, 45, 45, 1, 11, 10, 11, 11, 2, 2, 1, 1, 1, 9, 9, 45, 38, 45, 1, 11] 201
rigid atoms, others: [32, 33, 39, 9, 10, 11, 12, 13, 14, 15, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 40])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037417 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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, 201, 53, 53, 34, 34, 33, 34, 34, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 34, 201, 201, 201, 201, 53, 53, 33, 34, 34, 17, 17, 1, 1, 1, 34, 201] 201
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40])
total number of confs: 305
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037417 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 67, 201, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 6, 6, 11, 11, 11, 67, 67, 201, 201, 201, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 416
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037417 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037417
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037417/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037417
Building REAL300000037418
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037418'
/scratch/stefan/7769618/working/building/REAL300000037418 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037418

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037418/0 /scratch/stefan/7769618/working/building/REAL300000037418 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/463
`/scratch/stefan/7769618/working/3D/463' -> `0.mol2'
Preparing input files

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

`REAL300000037418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037418 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [11, 9, 11, 9, 5, 1, 1, 1, 1, 1, 1, 1, 9, 69, 69, 144, 136, 69, 144, 144, 1, 1, 9, 9, 9, 5, 5, 1, 1, 9, 9, 144, 69, 144, 1, 1, 9, 9] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 454
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037418 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 151, 94, 64, 33, 94, 94, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201, 201, 201, 151, 151, 94, 94, 33, 33, 1, 1, 1, 94, 94, 201, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 772
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037418 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 62, 199, 199, 201, 189, 199, 201, 201, 9, 9, 1, 1, 1, 5, 5, 9, 9, 62, 62, 201, 199, 201, 9, 9, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 22, 23, 24, 36, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 446
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037418 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037418
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037418/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037418
Building REAL300000037419
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037419'
/scratch/stefan/7769618/working/building/REAL300000037419 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037419

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037419/0 /scratch/stefan/7769618/working/building/REAL300000037419 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/464
`/scratch/stefan/7769618/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=NC=CC=N2)C(OCC(=O)[O-])=C1)

`REAL300000037419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037419 none COC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [129, 100, 79, 100, 100, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 100, 100, 152, 195, 201, 201, 100, 129, 129, 129, 100, 100, 56, 56, 1, 1, 1, 195, 195, 100] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
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: REAL300000037419 none COC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 6, 36, 37, 90, 88, 37, 90, 90, 1, 1, 7, 28, 56, 56, 1, 3, 3, 3, 1, 1, 6, 6, 90, 37, 90, 28, 28, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 15, 16, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037419 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037419
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037419/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037419
Building REAL300000037420
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037420'
/scratch/stefan/7769618/working/building/REAL300000037420 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037420

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037420/0 /scratch/stefan/7769618/working/building/REAL300000037420 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/465
`/scratch/stefan/7769618/working/3D/465' -> `0.mol2'
Preparing input files

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

`REAL300000037420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037420 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 200, 201, 150, 199, 200, 25, 25, 83, 83, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 25, 25, 1, 1, 1, 83, 83] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 670
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037420 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [22, 17, 22, 6, 17, 17, 1, 1, 1, 1, 1, 1, 8, 40, 41, 87, 84, 41, 87, 87, 1, 1, 1, 1, 8, 8, 87, 41, 87, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037420 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037420
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037420/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037420
Building REAL300000037421
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037421'
/scratch/stefan/7769618/working/building/REAL300000037421 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037421

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037421/0 /scratch/stefan/7769618/working/building/REAL300000037421 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/466
`/scratch/stefan/7769618/working/3D/466' -> `0.mol2'
Preparing input files

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

`REAL300000037421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037421 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 13, 13, 1, 1, 1] 38
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037421 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 38, 38, 34, 38, 38, 2, 2, 2, 1, 7, 7, 38, 34, 38] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037421 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037421
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037421/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037421
Building REAL300000037422
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037422'
/scratch/stefan/7769618/working/building/REAL300000037422 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037422

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037422/0 /scratch/stefan/7769618/working/building/REAL300000037422 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/467
`/scratch/stefan/7769618/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1Br)

`REAL300000037422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037422 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 137, 88, 56, 88, 88, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 201, 201, 88, 88, 33, 33, 1, 1, 1, 88] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
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: REAL300000037422 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [38, 22, 38, 7, 1, 1, 1, 1, 1, 1, 7, 39, 39, 94, 94, 39, 94, 94, 1, 1, 1, 22, 22, 1, 1, 7, 7, 94, 49, 94, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 416
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037422 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037422
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037422/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037422
Building REAL300000037423
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037423'
/scratch/stefan/7769618/working/building/REAL300000037423 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037423

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037423/0 /scratch/stefan/7769618/working/building/REAL300000037423 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/468
`/scratch/stefan/7769618/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=N2)C=C1)

`REAL300000037423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037423 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 44, 44, 1, 1, 1, 81, 81] 81
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037423 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 52, 52, 81, 81, 52, 81, 81, 1, 1, 4, 4, 4, 1, 9, 9, 81, 60, 81, 1, 1] 81
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 21, 22, 26] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037423 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037423
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037423/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037423
Building REAL300000037424
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037424'
/scratch/stefan/7769618/working/building/REAL300000037424 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037424

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037424/0 /scratch/stefan/7769618/working/building/REAL300000037424 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/469
`/scratch/stefan/7769618/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=NC=CC=N3)C=C2Cl)N=N1)

`REAL300000037424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037424 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=NC=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 28, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 36, 36, 55, 55, 36, 55, 55, 1, 1, 1, 28, 28, 28, 8, 8, 8, 8, 1, 1, 7, 7, 55, 36, 55, 1] 201
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037424 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=NC=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 148, 148, 143, 58, 33, 59, 59, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 201, 201, 201, 148, 148, 148, 148, 59, 59, 20, 20, 1, 1, 1, 59] 201
rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037424 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=NC=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 28, 14, 20, 114, 201, 201, 201, 201, 201, 201, 201, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 28, 28, 114, 114, 201, 201, 201, 28] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037424 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037424
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037424/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037424
Building REAL300000037425
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037425'
/scratch/stefan/7769618/working/building/REAL300000037425 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037425

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037425/0 /scratch/stefan/7769618/working/building/REAL300000037425 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/470
`/scratch/stefan/7769618/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000037425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037425 none COC1=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [66, 43, 43, 43, 42, 7, 7, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 94, 105, 105, 105, 66, 66, 66, 43, 42, 42, 1, 1, 1, 43, 105, 105] 105
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 31] 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, 34, 35, 36])
total number of confs: 324
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: REAL300000037425 none COC1=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 4, 12, 12, 41, 41, 12, 41, 41, 1, 1, 2, 2, 1, 1, 1, 9, 19, 31, 31, 4, 4, 4, 1, 4, 4, 41, 12, 41, 1, 19, 19] 107
rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 18, 19, 20, 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, 35, 36])
total number of confs: 212
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037425 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037425
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037425/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037425
Building REAL300000037426
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037426'
/scratch/stefan/7769618/working/building/REAL300000037426 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037426

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037426/0 /scratch/stefan/7769618/working/building/REAL300000037426 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/471
`/scratch/stefan/7769618/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NC=CC=N1)

`REAL300000037426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037426 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [140, 122, 140, 177, 177, 177, 122, 122, 122, 122, 122, 122, 122, 122, 122, 68, 12, 12, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 177, 177, 122, 122, 122, 68, 68, 1, 1, 1] 177
rigid atoms, others: [35, 36, 37, 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])
total number of confs: 545
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: REAL300000037426 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 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: [4, 1, 4, 17, 26, 26, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 52, 53, 117, 112, 53, 117, 117, 4, 4, 4, 17, 17, 1, 1, 1, 7, 7, 117, 53, 117] 181
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])
total number of confs: 412
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037426 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037426
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037426/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037426
Building REAL300000037427
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037427'
/scratch/stefan/7769618/working/building/REAL300000037427 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037427

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037427/0 /scratch/stefan/7769618/working/building/REAL300000037427 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/472
`/scratch/stefan/7769618/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000037427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037427 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 36, 36, 105, 105, 36, 105, 105, 1, 1, 1, 1, 1, 9, 19, 19, 9, 9, 19, 19, 19, 19, 1, 1, 7, 7, 7, 7, 105, 36, 105, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 33, 40, 10, 11, 12, 13, 14, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 363
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037427 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [79, 19, 79, 199, 199, 201, 201, 199, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 79, 79, 79, 79, 201, 199, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 450
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037427 none CC(N=NC1=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 51, 108, 108, 74, 108, 192, 201, 201, 192, 192, 201, 201, 201, 201, 108, 108, 51, 51, 51, 51, 1, 1, 1, 108, 108, 201, 201, 201, 201, 108, 108] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 592
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037427 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037427
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037427/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037427
Building REAL300000037428
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037428'
/scratch/stefan/7769618/working/building/REAL300000037428 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037428

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037428/0 /scratch/stefan/7769618/working/building/REAL300000037428 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/473
`/scratch/stefan/7769618/working/3D/473' -> `0.mol2'
Preparing input files

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

`REAL300000037428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037428 none COC1=CC(CN=NC2=NC=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [85, 59, 59, 59, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 153, 188, 188, 201, 194, 85, 85, 85, 59, 17, 17, 1, 1, 1, 59, 59, 188, 188, 188, 188] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 566
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037428 none COC1=CC(CN=NC2=NC=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 38, 38, 72, 72, 39, 72, 72, 1, 1, 1, 1, 8, 12, 12, 21, 19, 3, 3, 3, 1, 6, 6, 72, 39, 72, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037428 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037428
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037428/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037428
Building REAL300000037429
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037429'
/scratch/stefan/7769618/working/building/REAL300000037429 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037429

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037429/0 /scratch/stefan/7769618/working/building/REAL300000037429 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/474
`/scratch/stefan/7769618/working/3D/474' -> `0.mol2'
Preparing input files

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

`REAL300000037429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037429 none CC(N=NC1=NC=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 16, 16, 36, 36, 16, 36, 36, 1, 1, 1, 1, 1, 1, 6, 18, 27, 41, 57, 57, 1, 5, 5, 5, 5, 36, 16, 36, 1, 1, 1, 18, 18, 27, 27, 42, 42, 1] 201
rigid atoms, others: [32, 1, 39, 10, 11, 12, 13, 14, 15, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 340
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: REAL300000037429 none CC(N=NC1=NC=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 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: [15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 15, 32, 32, 32, 32, 32, 79, 112, 153, 201, 201, 201, 32, 15, 15, 15, 15, 1, 1, 1, 32, 32, 32, 112, 112, 153, 153, 201, 201, 32] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 777
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037429 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037429
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037429/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037429
Building REAL300000037430
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037430'
/scratch/stefan/7769618/working/building/REAL300000037430 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037430

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037430/0 /scratch/stefan/7769618/working/building/REAL300000037430 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/475
`/scratch/stefan/7769618/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NC=CC=N1)

`REAL300000037430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037430 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 8, 43, 87, 88, 88, 88, 88, 88, 184, 201, 201, 201, 201, 88, 88, 8, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 88, 88, 88, 88, 88, 88, 201, 201, 201, 201, 88, 88, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 592
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037430 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 2, 1, 1, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1, 9, 34, 34, 87, 87, 34, 87, 87, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 87, 34, 87] 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])
total number of confs: 366
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037430 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037430
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037430/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037430
Building REAL300000037431
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037431'
/scratch/stefan/7769618/working/building/REAL300000037431 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037431

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037431/0 /scratch/stefan/7769618/working/building/REAL300000037431 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/476
`/scratch/stefan/7769618/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NC=CC=N1)

`REAL300000037431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037431 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 42, 82, 83, 83, 83, 83, 83, 152, 201, 201, 201, 83, 83, 8, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 83, 83, 83, 83, 83, 83, 201, 201, 83, 83, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 710
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: REAL300000037431 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 3, 1, 1, 1, 1, 1, 1, 6, 22, 43, 43, 1, 1, 10, 39, 39, 99, 99, 39, 99, 99, 10, 10, 10, 10, 4, 4, 3, 3, 1, 1, 22, 22, 1, 1, 99, 39, 99] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39])
total number of confs: 408
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037431 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037431
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037431/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037431
Building REAL300000037432
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037432'
/scratch/stefan/7769618/working/building/REAL300000037432 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037432

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037432/0 /scratch/stefan/7769618/working/building/REAL300000037432 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/477
`/scratch/stefan/7769618/working/3D/477' -> `0.mol2'
Preparing input files

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

`REAL300000037432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037432 none CC(N=NC1=NC=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 24, 24, 77, 77, 24, 77, 77, 1, 1, 1, 1, 1, 1, 11, 25, 25, 37, 37, 1, 7, 7, 7, 7, 77, 24, 77, 1, 1, 1, 25, 25, 25, 25, 1] 201
rigid atoms, others: [1, 36, 10, 11, 12, 13, 14, 15, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 332
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037432 none CC(N=NC1=NC=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 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: [36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 36, 85, 85, 85, 85, 85, 168, 201, 201, 201, 201, 85, 36, 36, 36, 36, 1, 1, 1, 85, 85, 85, 201, 201, 201, 201, 85] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 504
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037432 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037432
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037432/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037432
Building REAL300000037433
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037433'
/scratch/stefan/7769618/working/building/REAL300000037433 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037433

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037433/0 /scratch/stefan/7769618/working/building/REAL300000037433 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/478
`/scratch/stefan/7769618/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NC=CC=N1)

`REAL300000037433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037433 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 8, 36, 62, 62, 62, 62, 62, 62, 140, 185, 201, 201, 195, 62, 62, 8, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 62, 62, 62, 62, 62, 62, 185, 185, 201, 201, 62, 62, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 691
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: REAL300000037433 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 1, 1, 1, 1, 1, 1, 1, 6, 22, 26, 43, 36, 1, 1, 9, 35, 35, 92, 92, 35, 92, 92, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 22, 22, 26, 26, 1, 1, 92, 35, 92] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 397
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037433 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037433
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037433/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037433
Building REAL300000037434
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037434'
/scratch/stefan/7769618/working/building/REAL300000037434 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037434

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037434/0 /scratch/stefan/7769618/working/building/REAL300000037434 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/479
`/scratch/stefan/7769618/working/3D/479' -> `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=NC=CC=N1)

`REAL300000037434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037434 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 8, 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, 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: [86, 28, 22, 8, 8, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 86, 196, 196, 201, 201, 196, 201, 201, 86, 86, 86, 86, 28, 28, 22, 22, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16, 201, 196, 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])
total number of confs: 591
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037434 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 8, 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, 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: [19, 7, 19, 28, 28, 28, 28, 28, 28, 43, 53, 201, 201, 201, 201, 201, 201, 201, 201, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 53, 53, 201, 201, 201, 201, 28, 28, 1, 1, 1] 201
rigid atoms, others: [47, 48, 49, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 365
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037434 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 8, 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, 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: [10, 4, 3, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 16, 1, 1, 10, 33, 33, 43, 43, 33, 43, 43, 10, 10, 10, 10, 4, 4, 3, 3, 1, 1, 2, 2, 16, 16, 16, 16, 1, 1, 43, 33, 43] 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])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037434 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037434
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037434/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037434
Building REAL300000037435
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037435'
/scratch/stefan/7769618/working/building/REAL300000037435 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037435

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037435/0 /scratch/stefan/7769618/working/building/REAL300000037435 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/480
`/scratch/stefan/7769618/working/3D/480' -> `0.mol2'
Preparing input files

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

`REAL300000037435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037435 none CCC(N=NC1=NC=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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: [4, 3, 1, 3, 7, 7, 20, 20, 7, 20, 20, 1, 1, 1, 1, 1, 6, 10, 26, 36, 59, 72, 75, 1, 1, 4, 4, 4, 4, 4, 3, 20, 7, 20, 1, 1, 10, 10, 26, 26, 36, 36, 59, 59, 1, 1] 201
rigid atoms, others: [34, 35, 44, 11, 12, 2, 14, 13, 23, 24, 45, 15] 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, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 402
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037435 none CCC(N=NC1=NC=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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: [12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 12, 12, 48, 70, 125, 163, 201, 200, 201, 18, 18, 12, 12, 12, 12, 12, 12, 1, 1, 1, 18, 18, 70, 70, 125, 125, 163, 163, 201, 201, 18, 18] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 929
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037435 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037435
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037435/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037435
Building REAL300000037436
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037436'
/scratch/stefan/7769618/working/building/REAL300000037436 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037436

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037436/0 /scratch/stefan/7769618/working/building/REAL300000037436 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/481
`/scratch/stefan/7769618/working/3D/481' -> `0.mol2'
Preparing input files

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

`REAL300000037436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037436 none COC1=CC(C(C)N=NC2=NC=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [68, 44, 44, 44, 14, 6, 14, 6, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 124, 176, 180, 201, 201, 201, 68, 68, 68, 44, 14, 14, 14, 14, 1, 1, 1, 44, 44, 176, 176, 180, 180, 201, 201] 201
rigid atoms, others: [33, 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, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 622
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037436 none COC1=CC(C(C)N=NC2=NC=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 6, 6, 20, 20, 53, 53, 20, 53, 53, 1, 1, 1, 1, 7, 16, 18, 30, 41, 41, 3, 3, 3, 1, 6, 6, 6, 6, 53, 20, 53, 1, 1, 16, 16, 18, 18, 30, 30] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 36, 28, 37] 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, 38, 39, 40, 41, 42, 43])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037436 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037436
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037436/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037436
Building REAL300000037437
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037437'
/scratch/stefan/7769618/working/building/REAL300000037437 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037437

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037437/0 /scratch/stefan/7769618/working/building/REAL300000037437 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/482
`/scratch/stefan/7769618/working/3D/482' -> `0.mol2'
Preparing input files

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

`REAL300000037437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037437 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 35, 35, 26, 35, 35, 11, 1, 1, 1, 1, 11, 11, 11, 35, 26, 35, 11, 11] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 110
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037437 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [18, 15, 18, 15, 15, 35, 35, 35, 35, 35, 35, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 15, 15, 15, 1, 1, 1, 15, 15] 35
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 75
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037437 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 16, 16, 8, 16, 16, 1, 11, 11, 11, 11, 1, 1, 1, 16, 8, 16, 1, 1] 35
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 60
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037437 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037437
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037437/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037437
Building REAL300000037438
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037438'
/scratch/stefan/7769618/working/building/REAL300000037438 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037438

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037438/0 /scratch/stefan/7769618/working/building/REAL300000037438 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/483
`/scratch/stefan/7769618/working/3D/483' -> `0.mol2'
Preparing input files

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

`REAL300000037438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037438 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 34, 34, 28, 34, 34, 10, 1, 1, 1, 1, 10, 10, 10, 34, 28, 34, 10, 10] 34
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 96
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037438 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [24, 21, 24, 21, 21, 35, 35, 35, 35, 35, 35, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 35, 21, 21, 21, 1, 1, 1, 21, 21] 35
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 77
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037438 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 19, 19, 9, 19, 19, 1, 10, 10, 10, 10, 1, 1, 1, 19, 9, 19, 1, 1] 34
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 67
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037438 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037438
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037438/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037438
Building REAL300000037439
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037439'
/scratch/stefan/7769618/working/building/REAL300000037439 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037439

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037439/0 /scratch/stefan/7769618/working/building/REAL300000037439 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/484
`/scratch/stefan/7769618/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=N1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000037439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037439 none CC(N=NC1=NC=CC=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 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]
0  hydrogens 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, 27, 27, 97, 97, 27, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 70, 70, 6, 6, 6, 6, 97, 27, 97, 1, 1, 1, 39, 39] 201
rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 481
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: REAL300000037439 none CC(N=NC1=NC=CC=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 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]
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: [56, 12, 12, 1, 1, 1, 1, 1, 1, 1, 56, 95, 95, 95, 56, 95, 95, 95, 153, 169, 169, 169, 56, 56, 56, 56, 1, 1, 1, 95, 95, 95, 169, 169] 169
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 600
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037439 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037439
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037439/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037439
Building REAL300000037440
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037440'
/scratch/stefan/7769618/working/building/REAL300000037440 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037440

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037440/0 /scratch/stefan/7769618/working/building/REAL300000037440 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/485
`/scratch/stefan/7769618/working/3D/485' -> `0.mol2'
Preparing input files

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

`REAL300000037440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037440 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NC=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 23, 9, 23, 9, 1, 1, 1, 1, 1, 1, 1, 36, 36, 39, 39, 39, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 1, 1, 1, 39, 39] 39
rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
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: REAL300000037440 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NC=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 27, 34, 34, 27, 34, 34, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 34, 27, 34, 3, 3] 39
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])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037440 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037440
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037440/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037440
Building REAL300000037441
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037441'
/scratch/stefan/7769618/working/building/REAL300000037441 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037441

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037441/0 /scratch/stefan/7769618/working/building/REAL300000037441 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/486
`/scratch/stefan/7769618/working/3D/486' -> `0.mol2'
Preparing input files

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

`REAL300000037441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037441 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 121, 58, 57, 57, 57, 57, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 57, 58, 57, 22, 22, 1, 1, 1, 58, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 644
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037441 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 3, 8, 32, 32, 8, 32, 32, 87, 201, 201, 201, 186, 201, 201, 201, 32, 1, 1, 1, 1, 1, 1, 3, 32, 32, 10, 87, 87, 201, 201, 201, 32, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 36, 37, 38, 39, 40, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 540
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037441 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 25, 29, 9, 1, 1, 1, 1, 1, 1, 1, 6, 34, 35, 57, 53, 35, 57, 57, 1, 25, 32, 32, 25, 32, 32, 25, 1, 1, 1, 6, 6, 57, 35, 57, 1, 32, 32, 25, 32, 32] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 19, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 297
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037441 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037441
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037441/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037441
Building REAL300000037442
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037442'
/scratch/stefan/7769618/working/building/REAL300000037442 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037442

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037442/0 /scratch/stefan/7769618/working/building/REAL300000037442 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/487
`/scratch/stefan/7769618/working/3D/487' -> `0.mol2'
Preparing input files

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

`REAL300000037442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037442 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 80, 80, 80, 80, 80, 80, 80, 80, 80, 46, 12, 46, 12, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 80, 80, 80, 46, 46, 46, 46, 1, 1, 1] 93
rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 229
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: REAL300000037442 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 52, 52, 111, 111, 52, 111, 111, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 111, 53, 111] 134
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 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: 354
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037442 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037442
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037442/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037442
Building REAL300000037443
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037443'
/scratch/stefan/7769618/working/building/REAL300000037443 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037443

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037443/0 /scratch/stefan/7769618/working/building/REAL300000037443 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/488
`/scratch/stefan/7769618/working/3D/488' -> `0.mol2'
Preparing input files

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

`REAL300000037443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037443 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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
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, 3, 3, 1, 1, 1, 1, 1, 1, 7, 25, 26, 32, 31, 26, 32, 32, 1, 1, 3, 3, 3, 3, 1, 1, 7, 7, 32, 26, 32, 1, 1, 3, 3] 37
rigid atoms, others: [34, 33, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037443 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 33, 37, 33, 37, 37, 32, 26, 32, 32, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 37, 37, 37, 37, 32, 32, 22, 22, 1, 1, 1, 32, 32, 37, 37] 37
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 150
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037443 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 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
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, 3, 3, 1, 2, 12, 37, 37, 37, 37, 37, 37, 37, 3, 3, 1, 1, 1, 1, 3, 3, 12, 12, 37, 37, 37, 3, 3, 1, 1] 37
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037443 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037443
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037443/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037443
Building REAL300000037444
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037444'
/scratch/stefan/7769618/working/building/REAL300000037444 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037444

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037444/0 /scratch/stefan/7769618/working/building/REAL300000037444 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/489
`/scratch/stefan/7769618/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037444 none COC1=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [120, 84, 83, 83, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 83, 83, 84, 83, 83, 171, 201, 201, 201, 201, 120, 120, 120, 83, 34, 34, 1, 1, 1, 84, 201, 201, 201, 201] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37])
total number of confs: 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: REAL300000037444 none COC1=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 54, 55, 104, 96, 55, 104, 104, 1, 1, 1, 1, 1, 5, 11, 11, 15, 15, 4, 4, 4, 1, 8, 8, 104, 55, 104, 1, 11, 11, 11, 11] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 359
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037444 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037444
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037444/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037444
Building REAL300000037445
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037445'
/scratch/stefan/7769618/working/building/REAL300000037445 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037445

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037445/0 /scratch/stefan/7769618/working/building/REAL300000037445 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/490
`/scratch/stefan/7769618/working/3D/490' -> `0.mol2'
Preparing input files

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

`REAL300000037445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037445 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [16, 13, 16, 12, 12, 1, 1, 1, 1, 1, 1, 8, 59, 59, 125, 119, 59, 125, 125, 1, 12, 12, 12, 12, 13, 1, 1, 8, 8, 125, 60, 125, 13, 13, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037445 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 128, 128, 128, 128, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 201, 201, 128, 128, 46, 46, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 770
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037445 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 59, 192, 192, 201, 198, 192, 201, 201, 12, 1, 1, 1, 1, 1, 13, 12, 58, 59, 201, 192, 201, 1, 1, 2] 402
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 435
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037445 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037445
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037445/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037445
Building REAL300000037446
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037446'
/scratch/stefan/7769618/working/building/REAL300000037446 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037446

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037446/0 /scratch/stefan/7769618/working/building/REAL300000037446 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/491
`/scratch/stefan/7769618/working/3D/491' -> `0.mol2'
Preparing input files

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

`REAL300000037446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037446 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 57, 57, 82, 79, 57, 82, 82, 1, 7, 7, 7, 7, 1, 1, 8, 8, 82, 57, 82, 7, 7] 119
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037446 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 93, 119, 119, 80, 80, 80, 80, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 80, 119, 119, 119, 119, 80, 80, 37, 37, 1, 1, 1, 119, 119] 119
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 335
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037446 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 47, 118, 118, 119, 116, 118, 119, 119, 8, 1, 1, 1, 1, 8, 8, 47, 47, 119, 118, 119, 1, 1] 119
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 265
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037446 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037446
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037446/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037446
Building REAL300000037447
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037447'
/scratch/stefan/7769618/working/building/REAL300000037447 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037447

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037447/0 /scratch/stefan/7769618/working/building/REAL300000037447 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/492
`/scratch/stefan/7769618/working/3D/492' -> `0.mol2'
Preparing input files

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

`REAL300000037447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037447 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 8, 58, 58, 108, 102, 59, 108, 108, 1, 11, 11, 11, 11, 1, 1, 8, 8, 108, 60, 108, 11] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 303
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037447 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 113, 113, 113, 113, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 113, 113, 40, 40, 1, 1, 1, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 367
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037447 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 11, 11, 11, 11, 65, 199, 199, 201, 189, 199, 201, 201, 11, 1, 1, 1, 1, 11, 11, 65, 65, 201, 199, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037447 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037447
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037447/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037447
Building REAL300000037448
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037448'
/scratch/stefan/7769618/working/building/REAL300000037448 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037448

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037448/0 /scratch/stefan/7769618/working/building/REAL300000037448 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/493
`/scratch/stefan/7769618/working/3D/493' -> `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=NC=CC=N2)=C1)

`REAL300000037448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037448 none O=C([O-])C1=CC=C(Br)C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 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, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 17, 17, 1, 1, 1, 42] 42
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
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: REAL300000037448 none O=C([O-])C1=CC=C(Br)C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 42, 42, 34, 42, 42, 1, 1, 1, 8, 8, 42, 34, 42, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037448 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037448
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037448/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037448
Building REAL300000037449
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037449'
/scratch/stefan/7769618/working/building/REAL300000037449 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037449

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037449/0 /scratch/stefan/7769618/working/building/REAL300000037449 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/494
`/scratch/stefan/7769618/working/3D/494' -> `0.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=NC=CC=N2)=C1)

`REAL300000037449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037449 none O=C([O-])C1=CC(Br)=C(O)C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 46, 46, 92, 24, 24, 1, 1, 1, 46] 92
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 27])
total number of confs: 196
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: REAL300000037449 none O=C([O-])C1=CC(Br)=C(O)C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 46, 46, 41, 46, 46, 1, 1, 2, 9, 9, 46, 41, 46, 1] 92
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 94
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037449 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037449/1 /scratch/stefan/7769618/working/building/REAL300000037449 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/495
`/scratch/stefan/7769618/working/3D/495' -> `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=NC=CC=N2)=C1)

`REAL300000037449.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037449/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037449 none O=C([O-])C1=CC(Br)=C([O-])C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 35, 35, 26, 26, 1, 1, 1, 35] 35
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 26])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037449 none O=C([O-])C1=CC(Br)=C([O-])C(CN=NC2=NC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 35, 35, 31, 35, 35, 1, 1, 6, 6, 35, 31, 35, 1] 35
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037449 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037449
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037449/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037449/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037449
Building REAL300000037450
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037450'
/scratch/stefan/7769618/working/building/REAL300000037450 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037450

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037450/0 /scratch/stefan/7769618/working/building/REAL300000037450 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/496
`/scratch/stefan/7769618/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(CN=NC2=NC=CC=N2)=C1OCC(=O)[O-])

`REAL300000037450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037450 none COC1=CC(Br)=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [151, 114, 114, 114, 114, 114, 114, 66, 10, 10, 1, 1, 1, 1, 1, 1, 1, 114, 114, 152, 200, 201, 201, 151, 151, 151, 114, 114, 66, 66, 1, 1, 1, 200, 200] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 30, 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, 33, 34])
total number of confs: 689
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: REAL300000037450 none COC1=CC(Br)=CC(CN=NC2=NC=CC=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 6, 38, 38, 103, 99, 38, 103, 103, 1, 1, 3, 14, 29, 29, 4, 4, 4, 1, 1, 6, 6, 103, 38, 103, 14, 14] 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])
total number of confs: 381
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037450 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037450
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037450/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037450
Building REAL300000037451
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037451'
/scratch/stefan/7769618/working/building/REAL300000037451 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037451

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037451/0 /scratch/stefan/7769618/working/building/REAL300000037451 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/497
`/scratch/stefan/7769618/working/3D/497' -> `0.mol2'
Preparing input files

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

`REAL300000037451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037451 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [9, 8, 9, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 68, 68, 151, 145, 68, 151, 151, 1, 1, 8, 8, 8, 1, 1, 1, 1, 9, 9, 151, 68, 151, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037451 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 201, 142, 114, 82, 49, 114, 114, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 142, 142, 114, 114, 49, 49, 1, 1, 1, 114, 114] 201
rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 718
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037451 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 8, 8, 8, 8, 8, 8, 63, 194, 194, 201, 197, 194, 201, 201, 8, 8, 1, 1, 1, 8, 8, 8, 8, 63, 63, 201, 194, 201, 8, 8] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 452
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037451 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037451
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037451/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037451
Building REAL300000037452
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037452'
/scratch/stefan/7769618/working/building/REAL300000037452 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037452

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037452/0 /scratch/stefan/7769618/working/building/REAL300000037452 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/498
`/scratch/stefan/7769618/working/3D/498' -> `0.mol2'
Preparing input files

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

`REAL300000037452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037452 none O=C([O-])C1=CC(I)=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 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, 60, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 59, 60, 60, 20, 20, 1, 1, 1, 60] 60
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
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: REAL300000037452 none O=C([O-])C1=CC(I)=CC(CN=NC2=NC=CC=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 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, 1, 8, 54, 54, 60, 60, 54, 60, 60, 1, 1, 1, 8, 8, 60, 54, 60, 1] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037452 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037452
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037452/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037452
Building REAL300000037453
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037453'
/scratch/stefan/7769618/working/building/REAL300000037453 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037453

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037453/0 /scratch/stefan/7769618/working/building/REAL300000037453 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/499
`/scratch/stefan/7769618/working/3D/499' -> `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=NC=CC=N2)=C1O)

`REAL300000037453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037453 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=NC=CC=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 54, 55, 55, 55, 55, 55, 55, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 55, 55, 54, 55, 55, 55, 55, 35, 35, 1, 1, 1, 110] 110
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 263
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: REAL300000037453 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=NC=CC=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 54, 53, 39, 54, 54, 1, 1, 1, 1, 1, 1, 1, 7, 7, 54, 39, 54, 2] 108
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31])
total number of confs: 146
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037453 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037453
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037453/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037453
Building REAL300000037454
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037454'
/scratch/stefan/7769618/working/building/REAL300000037454 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037454

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037454/0 /scratch/stefan/7769618/working/building/REAL300000037454 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/500
`/scratch/stefan/7769618/working/3D/500' -> `0.mol2'
Preparing input files

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

`REAL300000037454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037454 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
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, 64, 65, 104, 100, 65, 104, 104, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 104, 65, 104, 1, 1, 3] 191
rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 13, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39])
total number of confs: 310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037454 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [193, 193, 193, 158, 158, 157, 158, 158, 62, 41, 111, 111, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 111, 111, 158, 193, 193, 158, 158, 158, 111, 111, 41, 41, 1, 1, 1, 111, 112, 158] 193
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 735
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037454 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
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, 118, 118, 154, 146, 118, 154, 154, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 154, 118, 154, 3, 3, 1] 191
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037454 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037454
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037454/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037454
Building REAL300000037455
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037455'
/scratch/stefan/7769618/working/building/REAL300000037455 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037455

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037455/0 /scratch/stefan/7769618/working/building/REAL300000037455 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/501
`/scratch/stefan/7769618/working/3D/501' -> `0.mol2'
Preparing input files

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

`REAL300000037455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037455 none CCOC1=CC(CN=NC2=NC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [88, 83, 54, 54, 54, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 166, 199, 201, 201, 88, 88, 88, 88, 88, 54, 19, 19, 1, 1, 1, 54, 54, 199, 199] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 31] 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, 34, 35, 36, 37])
total number of confs: 529
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037455 none CCOC1=CC(CN=NC2=NC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 3, 1, 1, 1, 1, 1, 6, 36, 36, 72, 72, 37, 72, 72, 1, 1, 1, 1, 7, 20, 29, 29, 3, 3, 3, 3, 3, 1, 6, 6, 72, 38, 72, 1, 1, 20, 20] 201
rigid atoms, others: [2, 3, 4, 5, 6, 34, 15, 16, 17, 18, 35, 28] 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, 36, 37])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037455 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037455
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037455/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037455
Building REAL300000037456
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037456'
/scratch/stefan/7769618/working/building/REAL300000037456 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037456

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037456/0 /scratch/stefan/7769618/working/building/REAL300000037456 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/502
`/scratch/stefan/7769618/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=NC=CC=N1)

`REAL300000037456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037456 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 20, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 173, 173, 201, 186, 173, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 47, 47, 201, 173, 201] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 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, 32, 33, 34, 35, 36, 37])
total number of confs: 526
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037456 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [57, 53, 57, 53, 53, 53, 53, 93, 93, 93, 93, 93, 53, 44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 53, 44, 44, 1, 1, 1] 93
rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 313
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037456 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 13, 1, 1, 1, 6, 40, 40, 84, 80, 40, 84, 84, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 6, 6, 84, 40, 84] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037456 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037456
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037456/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037456
Building REAL300000037457
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037457'
/scratch/stefan/7769618/working/building/REAL300000037457 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037457

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037457/0 /scratch/stefan/7769618/working/building/REAL300000037457 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/503
`/scratch/stefan/7769618/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=N2)=C1C(=O)[O-])

`REAL300000037457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037457 none CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 54, 54, 55, 55, 55, 55, 55, 54, 54, 54, 40, 40, 1, 1, 1] 55
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037457 none CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 38, 38, 55, 54, 38, 55, 55, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 5, 5, 55, 38, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037457 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037457
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037457/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037457
Building REAL300000037458
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037458'
/scratch/stefan/7769618/working/building/REAL300000037458 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037458

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037458/0 /scratch/stefan/7769618/working/building/REAL300000037458 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/504
`/scratch/stefan/7769618/working/3D/504' -> `0.mol2'
Preparing input files

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

`REAL300000037458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037458 none CC(N=NC1=NC=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 20, 29, 29, 20, 29, 29, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 29, 20, 29, 1, 1, 1, 1] 29
rigid atoms, others: [32, 1, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037458 none CC(N=NC1=NC=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 1, 1, 1, 29, 29, 29, 29] 29
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037458 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037458
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037458/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037458
Building REAL300000037459
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037459'
/scratch/stefan/7769618/working/building/REAL300000037459 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037459

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037459/0 /scratch/stefan/7769618/working/building/REAL300000037459 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/505
`/scratch/stefan/7769618/working/3D/505' -> `0.mol2'
Preparing input files

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

`REAL300000037459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037459 none O=C([O-])C1=C(CN=NC2=NC=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 37, 37, 1, 1, 1, 60] 60
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 23])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037459 none O=C([O-])C1=C(CN=NC2=NC=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 6, 41, 41, 59, 59, 41, 59, 59, 1, 1, 1, 1, 6, 6, 59, 41, 59, 1] 59
rigid atoms, others: [1, 3, 4, 5, 14, 15, 16, 17, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037459 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037459
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037459/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037459
Building REAL300000037460
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037460'
/scratch/stefan/7769618/working/building/REAL300000037460 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037460

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037460/0 /scratch/stefan/7769618/working/building/REAL300000037460 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/506
`/scratch/stefan/7769618/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037460 none CC(N=NC1=NC=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 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
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 1, 1, 1, 1, 1] 14
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037460 none CC(N=NC1=NC=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 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
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 1, 1, 1, 14, 14, 14, 14, 14] 14
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 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: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037460 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037460
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037460/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037460
Building REAL300000037461
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037461'
/scratch/stefan/7769618/working/building/REAL300000037461 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037461

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037461/0 /scratch/stefan/7769618/working/building/REAL300000037461 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/507
`/scratch/stefan/7769618/working/3D/507' -> `0.mol2'
Preparing input files

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

`REAL300000037461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037461 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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: [44, 44, 44, 44, 44, 44, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 39, 40, 63, 61, 40, 63, 63, 44, 44, 44, 19, 19, 1, 1, 1, 1, 8, 8, 63, 40, 63] 201
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037461 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 1, 1, 1] 22
rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 64
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037461 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 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, 5, 21, 44, 44, 21, 44, 44, 44, 96, 201, 201, 201, 197, 201, 201, 201, 1, 1, 1, 5, 5, 44, 44, 21, 44, 96, 96, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 532
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037461 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037461
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037461/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037461
Building REAL300000037462
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037462'
/scratch/stefan/7769618/working/building/REAL300000037462 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037462

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037462/0 /scratch/stefan/7769618/working/building/REAL300000037462 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/508
`/scratch/stefan/7769618/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1CN=NC1=NC=CC=N1)

`REAL300000037462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037462 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 27, 27, 1, 1, 1] 35
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23])
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: REAL300000037462 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 34, 34, 35, 34, 34, 35, 35, 1, 1, 1, 6, 6, 35, 34, 35] 35
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037462 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037462
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037462/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037462
Building REAL300000037463
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037463'
/scratch/stefan/7769618/working/building/REAL300000037463 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037463

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037463/0 /scratch/stefan/7769618/working/building/REAL300000037463 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/509
`/scratch/stefan/7769618/working/3D/509' -> `0.mol2'
Preparing input files

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

`REAL300000037463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037463 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [96, 92, 92, 92, 92, 92, 112, 92, 92, 92, 92, 92, 92, 108, 108, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 92, 112, 112, 112, 92, 92, 65, 65, 1, 1, 1] 112
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 370
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037463 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=NC=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 36, 36, 91, 91, 36, 91, 91, 3, 3, 3, 1, 4, 4, 4, 1, 1, 4, 4, 91, 40, 91] 107
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 33, 28] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037463 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037463
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037463/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037463
Building REAL300000037464
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037464'
/scratch/stefan/7769618/working/building/REAL300000037464 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037464

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037464/0 /scratch/stefan/7769618/working/building/REAL300000037464 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/510
`/scratch/stefan/7769618/working/3D/510' -> `0.mol2'
Preparing input files

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

`REAL300000037464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037464 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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, 148, 95, 95, 95, 95, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 201, 201, 95, 95, 34, 34, 1, 1, 1, 95] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 577
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037464 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 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, 3, 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: [38, 21, 38, 7, 1, 1, 1, 1, 1, 1, 8, 40, 40, 90, 90, 42, 90, 90, 1, 1, 1, 21, 21, 1, 1, 8, 8, 90, 43, 90, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 375
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037464 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037464
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037464/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037464
Building REAL300000037465
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037465'
/scratch/stefan/7769618/working/building/REAL300000037465 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037465

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037465/0 /scratch/stefan/7769618/working/building/REAL300000037465 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/511
`/scratch/stefan/7769618/working/3D/511' -> `0.mol2'
Preparing input files

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

`REAL300000037465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037465 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=NC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 135, 135, 135, 135, 70, 135, 125, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 201, 135, 135, 40, 40, 1, 1, 1, 135, 135] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 760
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037465 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=NC=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 64, 65, 130, 122, 65, 130, 130, 1, 1, 9, 9, 5, 1, 1, 8, 8, 130, 65, 130, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 26, 27] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037465 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037465
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037465/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037465
Building REAL300000037466
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037466'
/scratch/stefan/7769618/working/building/REAL300000037466 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037466

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037466/0 /scratch/stefan/7769618/working/building/REAL300000037466 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/512
`/scratch/stefan/7769618/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(CN=NC3=NC=CC=N3)C(F)=CC=C2S1)

`REAL300000037466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037466 none O=C([O-])C1=CC2=C(CN=NC3=NC=CC=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 39, 40, 39, 39, 39, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 24, 24, 1, 1, 1, 39, 39] 40
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29])
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: REAL300000037466 none O=C([O-])C1=CC2=C(CN=NC3=NC=CC=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 8, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 39, 39, 40, 38, 39, 40, 40, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 39, 40, 1, 1] 40
rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037466 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037466
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037466/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037466
Building REAL300000037467
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037467'
/scratch/stefan/7769618/working/building/REAL300000037467 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037467

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037467/0 /scratch/stefan/7769618/working/building/REAL300000037467 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/513
`/scratch/stefan/7769618/working/3D/513' -> `0.mol2'
Preparing input files

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

`REAL300000037467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037467 none CC(N=NC1=CN=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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]
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, 9, 9, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 12, 12, 1, 1, 3, 3, 3, 3, 12, 12, 12, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 26
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 45, 46, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300000037467 none CC(N=NC1=CN=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [9, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 9, 9, 9, 9, 1, 1, 1, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12] 26
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037467 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037467/1 /scratch/stefan/7769618/working/building/REAL300000037467 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/514
`/scratch/stefan/7769618/working/3D/514' -> `1.mol2'
Preparing input files

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

`REAL300000037467.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037467/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037467 none CC(=NNC1=CN=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.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, 1, 8, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 63, 72, 92, 112, 112, 1, 1, 7, 7, 7, 19, 20, 20, 20, 1, 1, 27, 27, 27, 63, 63, 72, 72, 92, 92, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 45, 46, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 553
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: REAL300000037467 none CC(=NNC1=CN=CC=N1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.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, 1, 8, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 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]
0  hydrogens 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, 20, 20, 11, 20, 72, 72, 72, 135, 135, 170, 180, 201, 201, 201, 20, 20, 6, 6, 6, 2, 1, 1, 1, 20, 20, 135, 135, 135, 170, 170, 180, 178, 201, 201, 20, 20] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 828
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037467 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037467
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037467/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037467/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037467
Building REAL300000037468
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037468'
/scratch/stefan/7769618/working/building/REAL300000037468 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037468

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037468/0 /scratch/stefan/7769618/working/building/REAL300000037468 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/515
`/scratch/stefan/7769618/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000037468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037468 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 49, 49, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 7, 102, 102, 102, 1, 1, 12, 12, 1, 1] 162
rigid atoms, others: [32, 1, 35, 36, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037468 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 16, 102, 105, 162, 162, 162, 161, 162, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 16, 14, 16, 15, 162, 162, 161, 12, 12, 1, 1, 12, 12] 162
rigid atoms, others: [34, 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, 32, 35, 36])
total number of confs: 295
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037468 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 47, 102, 102, 54, 55, 162, 162, 162, 162, 162, 162, 162, 102, 102, 47, 47, 47, 47, 1, 1, 1, 102, 102, 162, 162, 102, 102] 162
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 1, 2, 10, 11, 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: 471
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037468 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037468
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037468/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037468
Building REAL300000037469
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037469'
/scratch/stefan/7769618/working/building/REAL300000037469 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037469

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037469/0 /scratch/stefan/7769618/working/building/REAL300000037469 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/516
`/scratch/stefan/7769618/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CN=CC=N2)=CC=C1OCC(=O)[O-])

`REAL300000037469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037469 none COC1=CC(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [103, 61, 61, 61, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 132, 201, 201, 201, 103, 103, 103, 61, 16, 16, 1, 1, 1, 61, 61, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 705
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037469 none COC1=CC(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 40, 40, 61, 61, 61, 61, 61, 1, 1, 1, 1, 9, 15, 19, 19, 3, 3, 3, 1, 6, 6, 61, 61, 61, 1, 1, 15, 15] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 14, 15, 16, 17, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037469 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037469
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037469/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037469
Building REAL300000037470
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037470'
/scratch/stefan/7769618/working/building/REAL300000037470 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037470

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037470/0 /scratch/stefan/7769618/working/building/REAL300000037470 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/517
`/scratch/stefan/7769618/working/3D/517' -> `0.mol2'
Preparing input files

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

`REAL300000037470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037470 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 23, 23, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 19, 19, 1, 1, 5, 5, 5, 5, 55, 55, 55, 1, 1, 9, 17, 17, 1, 1] 167
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037470 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 29, 55, 55, 29, 29, 96, 96, 96, 162, 167, 167, 167, 55, 55, 29, 29, 29, 29, 1, 1, 1, 55, 55, 162, 167, 167, 55, 55] 167
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 1, 2, 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])
total number of confs: 730
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037470 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037470/1 /scratch/stefan/7769618/working/building/REAL300000037470 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/518
`/scratch/stefan/7769618/working/3D/518' -> `1.mol2'
Preparing input files

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

`REAL300000037470.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037470/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037470 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 15, 15, 15, 15, 1, 1, 9, 17, 17, 1, 1] 51
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35])
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: REAL300000037470 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 6, 6, 28, 28, 28, 44, 51, 51, 51, 15, 15, 6, 6, 6, 2, 1, 1, 1, 15, 15, 44, 51, 51, 15, 15] 51
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 1, 2, 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])
total number of confs: 225
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037470 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037470
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037470/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037470/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037470
Building REAL300000037471
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037471'
/scratch/stefan/7769618/working/building/REAL300000037471 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037471

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037471/0 /scratch/stefan/7769618/working/building/REAL300000037471 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/519
`/scratch/stefan/7769618/working/3D/519' -> `0.mol2'
Preparing input files

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

`REAL300000037471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037471 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 20, 20, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 4, 4, 4, 4, 37, 37, 37, 1, 1, 9, 9, 9, 9, 9, 1, 1] 82
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
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: REAL300000037471 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 22, 37, 37, 22, 22, 50, 50, 50, 82, 82, 82, 82, 82, 37, 37, 22, 22, 22, 22, 1, 1, 1, 37, 37, 82, 82, 82, 82, 82, 37, 37] 82
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037471 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037471/1 /scratch/stefan/7769618/working/building/REAL300000037471 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/520
`/scratch/stefan/7769618/working/3D/520' -> `1.mol2'
Preparing input files

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

`REAL300000037471.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037471/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037471 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 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: [32, 1, 33, 40, 10, 11, 12, 13, 14, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
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: REAL300000037471 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 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: [3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037471 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037471
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037471/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037471/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037471
Building REAL300000037472
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037472'
/scratch/stefan/7769618/working/building/REAL300000037472 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037472

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037472/0 /scratch/stefan/7769618/working/building/REAL300000037472 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/521
`/scratch/stefan/7769618/working/3D/521' -> `0.mol2'
Preparing input files

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

`REAL300000037472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037472 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 12, 12, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 18, 18, 18, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 38
rigid atoms, others: [1, 34, 43, 33, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
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: REAL300000037472 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 14, 14, 26, 26, 26, 38, 38, 38, 38, 38, 38, 18, 18, 14, 14, 14, 14, 1, 1, 1, 18, 18, 38, 38, 38, 38, 38, 38, 38, 18, 18] 38
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037472 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037472/1 /scratch/stefan/7769618/working/building/REAL300000037472 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/522
`/scratch/stefan/7769618/working/3D/522' -> `1.mol2'
Preparing input files

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

`REAL300000037472.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037472/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037472 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 9, 9, 9, 9, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 25
rigid atoms, others: [1, 34, 43, 33, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 39
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037472 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 8, 8, 17, 17, 17, 25, 25, 25, 25, 25, 25, 9, 9, 8, 8, 8, 2, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 9, 9] 25
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 97
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037472 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037472
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037472/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037472/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037472
Building REAL300000037473
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037473'
/scratch/stefan/7769618/working/building/REAL300000037473 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037473

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037473/0 /scratch/stefan/7769618/working/building/REAL300000037473 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/523
`/scratch/stefan/7769618/working/3D/523' -> `0.mol2'
Preparing input files

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

`REAL300000037473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037473 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
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, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 6, 6, 6, 1, 1, 5, 5, 5, 5, 1, 1] 11
rigid atoms, others: [1, 34, 33, 40, 10, 11, 12, 13, 14, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
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: REAL300000037473 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 4, 8, 8, 8, 11, 11, 11, 11, 11, 11, 6, 6, 4, 4, 4, 4, 1, 1, 1, 6, 6, 11, 11, 11, 11, 6, 6] 11
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037473 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037473/1 /scratch/stefan/7769618/working/building/REAL300000037473 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/524
`/scratch/stefan/7769618/working/3D/524' -> `1.mol2'
Preparing input files

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

`REAL300000037473.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037473/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037473 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 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] 5
rigid atoms, others: [1, 34, 33, 40, 10, 11, 12, 13, 14, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
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: REAL300000037473 none CC(=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 2, 2, 2, 2, 1, 1, 1, 3, 3, 5, 5, 5, 5, 3, 3] 5
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 20
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037473 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037473
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037473/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037473/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037473
Building REAL300000037474
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037474'
/scratch/stefan/7769618/working/building/REAL300000037474 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037474

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037474/0 /scratch/stefan/7769618/working/building/REAL300000037474 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/525
`/scratch/stefan/7769618/working/3D/525' -> `0.mol2'
Preparing input files

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

`REAL300000037474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037474 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 121, 56, 56, 56, 18, 56, 56, 56, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 56, 56, 56, 18, 18, 1, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27])
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: REAL300000037474 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [38, 22, 38, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 37, 38, 56, 56, 56, 56, 56, 22, 22, 1, 1, 1, 6, 6, 56, 56, 56] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 214
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037474 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037474
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037474/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037474
Building REAL300000037475
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037475'
/scratch/stefan/7769618/working/building/REAL300000037475 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037475

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037475/0 /scratch/stefan/7769618/working/building/REAL300000037475 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/526
`/scratch/stefan/7769618/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC=N2)=C1)

`REAL300000037475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037475 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [9, 6, 9, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 54, 55, 97, 97, 97, 97, 97, 1, 6, 6, 6, 6, 2, 2, 1, 1, 1, 8, 8, 97, 97, 97, 1] 201
rigid atoms, others: [32, 33, 34, 40, 10, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037475 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 133, 132, 97, 96, 96, 96, 96, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 132, 132, 96, 96, 96, 22, 22, 1, 1, 1, 96] 201
rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40])
total number of confs: 348
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037475 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 3, 6, 6, 3, 6, 6, 38, 140, 141, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 38, 38, 201, 201, 201, 6] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 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: 406
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037475 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037475
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037475/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037475
Building REAL300000037476
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037476'
/scratch/stefan/7769618/working/building/REAL300000037476 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037476

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037476/0 /scratch/stefan/7769618/working/building/REAL300000037476 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/527
`/scratch/stefan/7769618/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1[N+](=O)[O-])

`REAL300000037476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037476 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 9, 9, 9, 9, 9, 15, 15, 9, 9, 4, 2, 1, 1, 1, 9] 15
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
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: REAL300000037476 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 9, 9, 9, 9, 1] 15
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037476 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037476
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037476/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037476
Building REAL300000037477
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037477'
/scratch/stefan/7769618/working/building/REAL300000037477 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037477

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037477/0 /scratch/stefan/7769618/working/building/REAL300000037477 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/528
`/scratch/stefan/7769618/working/3D/528' -> `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=CN=CC=N3)C=C2)=C1)

`REAL300000037477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037477 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 51, 51, 82, 82, 82, 82, 82, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 82, 82, 82, 1, 1, 6] 201
rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 39, 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, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037477 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 83, 83, 40, 20, 83, 83, 19, 2, 2, 1, 1, 1, 1, 1, 1, 1, 82, 83, 201, 201, 201, 201, 83, 83, 83, 83, 19, 19, 1, 1, 1, 82, 83, 201] 201
rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 523
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037477 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 35, 145, 145, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 35, 35, 201, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 40, 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])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037477 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037477
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037477/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037477
Building REAL300000037478
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037478'
/scratch/stefan/7769618/working/building/REAL300000037478 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037478

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037478/0 /scratch/stefan/7769618/working/building/REAL300000037478 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/529
`/scratch/stefan/7769618/working/3D/529' -> `0.mol2'
Preparing input files

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

`REAL300000037478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037478 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 10, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 38, 38, 54, 54, 54, 54, 54, 1, 11, 10, 11, 11, 2, 2, 1, 1, 1, 8, 8, 54, 54, 54, 1, 11] 201
rigid atoms, others: [32, 33, 39, 9, 10, 11, 12, 13, 14, 15, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 40])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037478 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 82, 82, 54, 54, 54, 54, 54, 14, 2, 2, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 82, 82, 54, 54, 54, 14, 14, 1, 1, 1, 54, 201] 201
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40])
total number of confs: 333
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037478 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CN=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 51, 151, 151, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 6, 6, 11, 11, 11, 51, 51, 201, 201, 201, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037478 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037478
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037478/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037478
Building REAL300000037479
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037479'
/scratch/stefan/7769618/working/building/REAL300000037479 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037479

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037479/0 /scratch/stefan/7769618/working/building/REAL300000037479 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/530
`/scratch/stefan/7769618/working/3D/530' -> `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=CN=CC=N3)C=C2)OC=C1)

`REAL300000037479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037479 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [11, 9, 11, 9, 5, 1, 1, 1, 1, 1, 1, 1, 8, 64, 64, 119, 119, 119, 119, 119, 1, 1, 9, 9, 9, 5, 5, 1, 1, 8, 8, 119, 119, 119, 1, 1, 9, 9] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 216
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037479 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 133, 120, 63, 36, 120, 120, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 119, 120, 201, 201, 201, 133, 133, 120, 120, 35, 35, 1, 1, 1, 119, 120, 201, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 677
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037479 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 45, 157, 157, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 5, 5, 9, 9, 45, 45, 201, 201, 201, 9, 9, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 22, 23, 24, 36, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 398
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037479 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037479
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037479/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037479
Building REAL300000037480
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037480'
/scratch/stefan/7769618/working/building/REAL300000037480 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037480

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037480/0 /scratch/stefan/7769618/working/building/REAL300000037480 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/531
`/scratch/stefan/7769618/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=CN=CC=N2)C(OCC(=O)[O-])=C1)

`REAL300000037480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037480 none COC1=CC=C(CN=NC2=CN=CC=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [79, 67, 37, 67, 67, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 67, 67, 140, 197, 199, 199, 67, 79, 79, 79, 67, 67, 22, 22, 1, 1, 1, 197, 197, 67] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 671
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037480 none COC1=CC=C(CN=NC2=CN=CC=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 6, 38, 38, 67, 67, 67, 67, 67, 1, 1, 7, 22, 35, 35, 1, 3, 3, 3, 1, 1, 6, 6, 67, 67, 67, 22, 22, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 15, 16, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037480 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037480
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037480/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037480
Building REAL300000037481
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037481'
/scratch/stefan/7769618/working/building/REAL300000037481 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037481

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037481/0 /scratch/stefan/7769618/working/building/REAL300000037481 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/532
`/scratch/stefan/7769618/working/3D/532' -> `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=CN=CC=N2)C=C1)

`REAL300000037481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037481 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 161, 201, 201, 36, 17, 71, 71, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 16, 16, 1, 1, 1, 71, 71] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 611
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037481 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 12, 16, 5, 12, 12, 1, 1, 1, 1, 1, 1, 6, 41, 41, 71, 71, 71, 71, 71, 1, 1, 1, 1, 6, 6, 71, 71, 71, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037481 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037481
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037481/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037481
Building REAL300000037482
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037482'
/scratch/stefan/7769618/working/building/REAL300000037482 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037482

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037482/0 /scratch/stefan/7769618/working/building/REAL300000037482 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/533
`/scratch/stefan/7769618/working/3D/533' -> `0.mol2'
Preparing input files

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

`REAL300000037482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037482 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 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, 64, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 29, 29, 1, 1, 1] 64
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24])
total number of confs: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037482 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 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, 1, 7, 51, 51, 64, 64, 64, 64, 64, 2, 2, 2, 1, 7, 7, 64, 64, 64] 64
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037482 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037482/1 /scratch/stefan/7769618/working/building/REAL300000037482 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/534
`/scratch/stefan/7769618/working/3D/534' -> `1.mol2'
Preparing input files

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

`REAL300000037482.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037482/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037482 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 12, 12, 12, 12, 8, 4, 1, 1, 1] 12
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24])
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: REAL300000037482 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 2, 2, 2, 1, 8, 12, 12, 12, 12] 12
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 22] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037482 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037482
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037482/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037482/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037482
Building REAL300000037483
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037483'
/scratch/stefan/7769618/working/building/REAL300000037483 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037483

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037483/0 /scratch/stefan/7769618/working/building/REAL300000037483 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/535
`/scratch/stefan/7769618/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CN=CC=N2)C=C1Br)

`REAL300000037483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037483 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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, 183, 88, 33, 89, 89, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 201, 201, 89, 89, 19, 19, 1, 1, 1, 89] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
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: REAL300000037483 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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: [21, 17, 21, 7, 1, 1, 1, 1, 1, 1, 8, 50, 50, 89, 89, 89, 89, 89, 1, 1, 1, 17, 17, 1, 1, 8, 8, 89, 89, 89, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037483 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037483/1 /scratch/stefan/7769618/working/building/REAL300000037483 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/536
`/scratch/stefan/7769618/working/3D/536' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1Br)

`REAL300000037483.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037483/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037483 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 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, 115, 54, 30, 54, 54, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 164, 164, 54, 54, 17, 4, 1, 1, 1, 54] 164
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 497
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: REAL300000037483 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 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: [65, 44, 65, 9, 1, 1, 1, 1, 1, 1, 10, 10, 37, 54, 54, 54, 54, 54, 1, 1, 1, 44, 44, 1, 1, 10, 37, 54, 54, 54, 1] 164
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 329
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037483 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037483
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037483/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037483/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037483
Building REAL300000037484
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037484'
/scratch/stefan/7769618/working/building/REAL300000037484 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037484

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037484/0 /scratch/stefan/7769618/working/building/REAL300000037484 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/537
`/scratch/stefan/7769618/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC=N2)C=C1)

`REAL300000037484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037484 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 8, 2, 1, 1, 1, 15, 15] 15
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
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: REAL300000037484 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 14, 15, 15, 15, 15, 15, 1, 1, 3, 3, 3, 1, 7, 14, 15, 15, 15, 1, 1] 15
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 21, 22, 26] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037484 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037484/1 /scratch/stefan/7769618/working/building/REAL300000037484 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/538
`/scratch/stefan/7769618/working/3D/538' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC=N2)C=C1)

`REAL300000037484.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037484/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037484 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 41, 41, 1, 1, 1, 138, 138] 138
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037484 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 60, 60, 138, 138, 138, 138, 138, 1, 1, 3, 3, 3, 1, 8, 8, 138, 138, 138, 1, 1] 138
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 21, 22, 26] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037484 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037484
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037484/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037484/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037484
Building REAL300000037485
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037485'
/scratch/stefan/7769618/working/building/REAL300000037485 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037485

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037485/0 /scratch/stefan/7769618/working/building/REAL300000037485 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/539
`/scratch/stefan/7769618/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=CN=CC=N3)C=C2Cl)N=N1)

`REAL300000037485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 23, 23, 7, 7, 5, 1, 1, 1, 1, 1, 1, 7, 30, 30, 42, 42, 42, 42, 42, 1, 1, 1, 23, 23, 23, 7, 7, 7, 7, 1, 1, 7, 7, 42, 42, 42, 1] 201
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 128, 128, 116, 41, 28, 42, 42, 12, 2, 2, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 201, 201, 201, 128, 128, 128, 128, 42, 42, 12, 12, 1, 1, 1, 42] 201
rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 476
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(CN=NC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 23, 13, 15, 85, 172, 172, 201, 201, 201, 201, 201, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 23, 23, 85, 85, 201, 201, 201, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 536
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037485 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037485/1 /scratch/stefan/7769618/working/building/REAL300000037485 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/540
`/scratch/stefan/7769618/working/3D/540' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CN=CC=N3)C=C2Cl)N=N1)

`REAL300000037485.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037485/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 30, 9, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 15, 15, 15, 15, 1, 1, 1, 118, 118, 118, 38, 38, 30, 30, 1, 1, 6, 14, 15, 15, 15, 1] 201
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 295
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 137, 128, 70, 15, 7, 15, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 201, 201, 201, 137, 137, 128, 128, 15, 15, 4, 2, 1, 1, 1, 15] 201
rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 558
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037485 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CN=CC=N3)C=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 16, 60, 118, 118, 60, 76, 181, 195, 201, 201, 201, 201, 201, 201, 118, 118, 118, 1, 1, 1, 8, 8, 16, 16, 118, 118, 181, 201, 201, 201, 201, 118] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 711
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037485 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037485
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037485/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037485/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037485
Building REAL300000037486
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037486'
/scratch/stefan/7769618/working/building/REAL300000037486 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037486

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037486/0 /scratch/stefan/7769618/working/building/REAL300000037486 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/541
`/scratch/stefan/7769618/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CN=CC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000037486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037486 none COC1=CC(C=NNC2=CN=CC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [43, 23, 23, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 67, 88, 88, 88, 43, 43, 43, 23, 9, 3, 1, 1, 1, 23, 88, 88] 88
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 31] 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, 34, 35, 36])
total number of confs: 244
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: REAL300000037486 none COC1=CC(C=NNC2=CN=CC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 22, 23, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1, 1, 9, 17, 24, 24, 3, 4, 3, 1, 7, 22, 23, 23, 23, 1, 17, 17] 88
rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 18, 19, 20, 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, 35, 36])
total number of confs: 145
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037486 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037486
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037486/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037486
Building REAL300000037487
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037487'
/scratch/stefan/7769618/working/building/REAL300000037487 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037487

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037487/0 /scratch/stefan/7769618/working/building/REAL300000037487 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/542
`/scratch/stefan/7769618/working/3D/542' -> `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=CN=CC=N1)

`REAL300000037487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037487 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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: [133, 103, 133, 201, 201, 201, 103, 103, 103, 103, 103, 103, 103, 103, 103, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 103, 103, 103, 43, 43, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 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])
total number of confs: 668
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037487 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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: [4, 1, 4, 13, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 47, 48, 103, 103, 103, 103, 103, 4, 4, 4, 13, 13, 1, 1, 1, 7, 7, 103, 103, 103] 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])
total number of confs: 236
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037487 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037487
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037487/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037487
Building REAL300000037488
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037488'
/scratch/stefan/7769618/working/building/REAL300000037488 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037488

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037488/0 /scratch/stefan/7769618/working/building/REAL300000037488 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/543
`/scratch/stefan/7769618/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000037488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037488 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 29, 29, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 7, 7, 7, 7, 53, 53, 53, 1, 1, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [1, 34, 33, 40, 10, 11, 12, 13, 14, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037488 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [50, 8, 50, 136, 136, 201, 201, 201, 201, 201, 5, 17, 17, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 50, 50, 50, 48, 201, 201, 201, 17, 17, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 447
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037488 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 26, 53, 53, 35, 35, 176, 201, 201, 201, 201, 201, 201, 201, 201, 53, 53, 26, 26, 26, 26, 1, 1, 1, 53, 53, 201, 201, 201, 201, 53, 53] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037488 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037488
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037488/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037488
Building REAL300000037489
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037489'
/scratch/stefan/7769618/working/building/REAL300000037489 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037489

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037489/0 /scratch/stefan/7769618/working/building/REAL300000037489 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/544
`/scratch/stefan/7769618/working/3D/544' -> `0.mol2'
Preparing input files

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

`REAL300000037489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037489 none COC1=CC(CN=NC2=CN=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [97, 61, 61, 61, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 163, 194, 194, 201, 190, 97, 97, 97, 61, 16, 16, 1, 1, 1, 61, 61, 194, 194, 194, 194] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 516
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037489 none COC1=CC(CN=NC2=CN=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 38, 38, 61, 61, 61, 61, 61, 1, 1, 1, 1, 7, 11, 11, 19, 17, 3, 3, 3, 1, 6, 6, 61, 61, 61, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037489 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037489
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037489/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037489
Building REAL300000037490
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037490'
/scratch/stefan/7769618/working/building/REAL300000037490 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037490

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037490/0 /scratch/stefan/7769618/working/building/REAL300000037490 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/545
`/scratch/stefan/7769618/working/3D/545' -> `0.mol2'
Preparing input files

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

`REAL300000037490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037490 none CC(N=NC1=CN=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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, 1, 6, 21, 21, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 6, 16, 18, 30, 39, 39, 1, 6, 6, 6, 6, 35, 35, 35, 1, 1, 1, 17, 17, 17, 17, 30, 30, 1] 201
rigid atoms, others: [32, 1, 39, 10, 11, 12, 13, 14, 15, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 222
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: REAL300000037490 none CC(N=NC1=CN=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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, 10, 35, 35, 35, 35, 35, 114, 139, 139, 201, 201, 201, 35, 10, 10, 10, 10, 1, 1, 1, 35, 35, 35, 139, 139, 139, 139, 201, 201, 35] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 656
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037490 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037490/1 /scratch/stefan/7769618/working/building/REAL300000037490 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/546
`/scratch/stefan/7769618/working/3D/546' -> `1.mol2'
Preparing input files

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

`REAL300000037490.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037490/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037490 none CC(=NNC1=CN=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 7, 23, 37, 56, 75, 75, 1, 11, 11, 11, 28, 28, 28, 28, 1, 1, 1, 23, 23, 37, 37, 56, 56, 1] 201
rigid atoms, others: [32, 1, 39, 10, 11, 12, 13, 14, 15, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 386
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: REAL300000037490 none CC(=NNC1=CN=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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, 6, 28, 28, 28, 28, 28, 80, 121, 161, 201, 201, 201, 28, 6, 6, 6, 2, 1, 1, 1, 28, 28, 28, 121, 121, 161, 161, 201, 201, 28] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 751
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037490 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037490
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037490/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037490/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037490
Building REAL300000037491
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037491'
/scratch/stefan/7769618/working/building/REAL300000037491 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037491

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037491/0 /scratch/stefan/7769618/working/building/REAL300000037491 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/547
`/scratch/stefan/7769618/working/3D/547' -> `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=CN=CC=N1)

`REAL300000037491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037491 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 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: [25, 5, 25, 57, 63, 63, 63, 63, 63, 170, 201, 201, 201, 201, 63, 63, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 61, 61, 63, 62, 63, 63, 201, 201, 201, 201, 63, 63, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 596
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037491 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 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: [9, 3, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 35, 35, 1, 1, 9, 34, 34, 63, 63, 63, 63, 63, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 63, 63, 63] 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])
total number of confs: 227
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037491 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037491
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037491/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037491
Building REAL300000037492
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037492'
/scratch/stefan/7769618/working/building/REAL300000037492 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037492

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037492/0 /scratch/stefan/7769618/working/building/REAL300000037492 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/548
`/scratch/stefan/7769618/working/3D/548' -> `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=CN=CC=N1)

`REAL300000037492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037492 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 61, 70, 70, 70, 70, 70, 148, 201, 201, 201, 70, 70, 5, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 68, 68, 70, 68, 70, 70, 201, 201, 70, 70, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 713
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: REAL300000037492 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 35, 35, 1, 1, 8, 38, 38, 70, 70, 70, 70, 70, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 23, 23, 1, 1, 70, 70, 70] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39])
total number of confs: 235
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037492 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037492
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037492/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037492
Building REAL300000037493
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037493'
/scratch/stefan/7769618/working/building/REAL300000037493 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037493

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037493/0 /scratch/stefan/7769618/working/building/REAL300000037493 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/549
`/scratch/stefan/7769618/working/3D/549' -> `0.mol2'
Preparing input files

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

`REAL300000037493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037493 none CC(N=NC1=CN=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 10, 25, 25, 32, 32, 1, 6, 6, 6, 6, 56, 56, 56, 1, 1, 1, 25, 25, 25, 25, 1] 201
rigid atoms, others: [1, 36, 10, 11, 12, 13, 14, 15, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
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: REAL300000037493 none CC(N=NC1=CN=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 19, 56, 56, 56, 56, 56, 153, 201, 201, 201, 201, 56, 19, 19, 19, 19, 1, 1, 1, 56, 56, 56, 201, 201, 201, 201, 56] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 504
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037493 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037493
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037493/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037493
Building REAL300000037494
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037494'
/scratch/stefan/7769618/working/building/REAL300000037494 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037494

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037494/0 /scratch/stefan/7769618/working/building/REAL300000037494 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/550
`/scratch/stefan/7769618/working/3D/550' -> `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=CN=CC=N1)

`REAL300000037494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037494 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 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: [32, 6, 32, 61, 71, 71, 71, 71, 71, 192, 201, 201, 201, 201, 71, 71, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 68, 68, 71, 69, 71, 71, 201, 201, 201, 201, 71, 71, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 533
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: REAL300000037494 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 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: [9, 3, 2, 1, 1, 1, 1, 1, 1, 6, 21, 22, 29, 28, 1, 1, 9, 38, 38, 71, 71, 71, 71, 71, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 21, 22, 21, 21, 1, 1, 71, 71, 71] 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])
total number of confs: 221
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037494 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037494
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037494/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037494
Building REAL300000037495
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037495'
/scratch/stefan/7769618/working/building/REAL300000037495 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037495

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037495/0 /scratch/stefan/7769618/working/building/REAL300000037495 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/551
`/scratch/stefan/7769618/working/3D/551' -> `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=CN=CC=N1)

`REAL300000037495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037495 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 22, 16, 8, 8, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 63, 127, 127, 201, 201, 201, 201, 201, 63, 63, 63, 63, 22, 22, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16, 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])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037495 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 34, 34, 34, 34, 34, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 34, 34, 34, 34, 34, 34, 57, 57, 201, 201, 201, 201, 34, 34, 1, 1, 1] 201
rigid atoms, others: [47, 48, 49, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 377
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037495 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 2, 1, 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, 2, 2, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 1, 1, 34, 34, 34] 201
rigid atoms, others: [19, 2, 35, 4, 5, 6, 7, 8, 45, 46, 3, 20, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 47, 48, 49])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037495 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037495
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037495/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037495
Building REAL300000037496
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037496'
/scratch/stefan/7769618/working/building/REAL300000037496 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037496

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037496/0 /scratch/stefan/7769618/working/building/REAL300000037496 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/552
`/scratch/stefan/7769618/working/3D/552' -> `0.mol2'
Preparing input files

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

`REAL300000037496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037496 none CCC(N=NC1=CN=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 10, 10, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 6, 10, 24, 31, 53, 59, 62, 1, 1, 5, 5, 5, 5, 5, 4, 19, 19, 19, 1, 1, 10, 10, 23, 23, 32, 32, 52, 52, 1, 1] 201
rigid atoms, others: [34, 35, 44, 11, 12, 2, 14, 13, 23, 24, 45, 15] 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, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 311
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037496 none CCC(N=NC1=CN=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 12, 19, 19, 13, 18, 88, 96, 144, 153, 192, 196, 201, 19, 19, 19, 19, 19, 19, 19, 12, 1, 1, 1, 19, 19, 96, 96, 144, 144, 153, 153, 192, 192, 19, 19] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 769
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037496 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037496
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037496/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037496
Building REAL300000037497
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037497'
/scratch/stefan/7769618/working/building/REAL300000037497 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037497

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037497/0 /scratch/stefan/7769618/working/building/REAL300000037497 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/553
`/scratch/stefan/7769618/working/3D/553' -> `0.mol2'
Preparing input files

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

`REAL300000037497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037497 none COC1=CC(C(C)N=NC2=CN=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [69, 41, 41, 41, 12, 3, 12, 3, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 123, 184, 184, 201, 201, 201, 69, 69, 69, 41, 12, 12, 12, 12, 1, 1, 1, 41, 41, 184, 184, 184, 184, 201, 201] 201
rigid atoms, others: [33, 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, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037497 none COC1=CC(C(C)N=NC2=CN=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 6, 6, 23, 23, 41, 41, 41, 41, 41, 1, 1, 1, 1, 7, 12, 12, 19, 25, 25, 3, 3, 3, 1, 6, 6, 6, 6, 41, 41, 41, 1, 1, 12, 12, 12, 12, 19, 19] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 36, 28, 37] 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, 38, 39, 40, 41, 42, 43])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037497 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037497/1 /scratch/stefan/7769618/working/building/REAL300000037497 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/554
`/scratch/stefan/7769618/working/3D/554' -> `1.mol2'
Preparing input files

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

`REAL300000037497.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037497/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037497 none COC1=CC(C(C)=NNC2=CN=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 30, 30, 30, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 93, 169, 177, 201, 201, 201, 50, 50, 50, 30, 6, 6, 6, 2, 1, 1, 1, 30, 30, 169, 169, 177, 177, 201, 201] 201
rigid atoms, others: [33, 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, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 698
number of broken/clashed sets: 138
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037497 none COC1=CC(C(C)=NNC2=CN=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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, 1, 1, 1, 1, 8, 27, 33, 44, 58, 58, 4, 4, 4, 1, 11, 11, 11, 30, 30, 30, 30, 1, 1, 27, 27, 33, 33, 44, 44] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 36, 28, 37] 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, 38, 39, 40, 41, 42, 43])
total number of confs: 330
number of broken/clashed sets: 138
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037497 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037497
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037497/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037497/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037497
Building REAL300000037498
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037498'
/scratch/stefan/7769618/working/building/REAL300000037498 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037498

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037498/0 /scratch/stefan/7769618/working/building/REAL300000037498 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/555
`/scratch/stefan/7769618/working/3D/555' -> `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=CN=CC=N2)C1)

`REAL300000037498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037498 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5] 20
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 39
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037498 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 10, 10, 10, 1, 1, 1, 10, 10] 20
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 39
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037498 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 1, 5, 5, 5, 5, 1, 1, 1, 10, 10, 10, 1, 1] 20
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 24
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037498 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037498
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037498/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037498
Building REAL300000037499
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037499'
/scratch/stefan/7769618/working/building/REAL300000037499 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037499

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037499/0 /scratch/stefan/7769618/working/building/REAL300000037499 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/556
`/scratch/stefan/7769618/working/3D/556' -> `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=CN=CC=N2)C1)

`REAL300000037499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037499 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5] 20
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 39
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037499 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 10, 10, 10, 1, 1, 1, 10, 10] 20
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 39
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037499 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 1, 5, 5, 5, 5, 1, 1, 1, 10, 10, 10, 1, 1] 20
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 24
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037499 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037499
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037499/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037499
Building REAL300000037500
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037500'
/scratch/stefan/7769618/working/building/REAL300000037500 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037500

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037500/0 /scratch/stefan/7769618/working/building/REAL300000037500 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/557
`/scratch/stefan/7769618/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC=N1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000037500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037500 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [6, 1, 6, 26, 26, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 48, 48, 6, 6, 6, 6, 56, 56, 56, 1, 1, 1, 31, 31] 201
rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
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: REAL300000037500 none CC(N=NC1=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 25, 56, 56, 56, 25, 56, 56, 56, 149, 201, 201, 201, 25, 25, 25, 25, 1, 1, 1, 56, 56, 56, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 667
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037500 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037500
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037500/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037500
Building REAL300000037501
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037501'
/scratch/stefan/7769618/working/building/REAL300000037501 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037501

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037501/0 /scratch/stefan/7769618/working/building/REAL300000037501 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/558
`/scratch/stefan/7769618/working/3D/558' -> `0.mol2'
Preparing input files

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

`REAL300000037501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037501 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 60, 32, 6, 32, 6, 1, 1, 1, 1, 1, 1, 1, 60, 60, 74, 74, 74, 60, 60, 60, 60, 60, 60, 32, 32, 32, 32, 1, 1, 1, 74, 74] 74
rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
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: REAL300000037501 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CN=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 60, 60, 60, 60, 60, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 60, 60, 60, 3, 3] 74
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])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037501 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037501
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037501/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037501
Building REAL300000037502
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037502'
/scratch/stefan/7769618/working/building/REAL300000037502 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037502

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037502/0 /scratch/stefan/7769618/working/building/REAL300000037502 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/559
`/scratch/stefan/7769618/working/3D/559' -> `0.mol2'
Preparing input files

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

`REAL300000037502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037502 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 117, 45, 45, 45, 45, 45, 15, 2, 2, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 15, 15, 1, 1, 1, 45, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037502 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 3, 6, 18, 18, 14, 18, 18, 77, 177, 177, 201, 201, 201, 201, 201, 18, 1, 1, 1, 1, 1, 1, 3, 18, 18, 15, 77, 77, 201, 201, 201, 18, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 36, 37, 38, 39, 40, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 461
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037502 none O=C([O-])C(OC1=CC=CC(CN=NC2=CN=CC=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 45, 45, 45, 45, 45, 1, 17, 18, 18, 17, 18, 18, 17, 1, 1, 1, 7, 7, 45, 45, 45, 1, 18, 18, 17, 18, 18] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 19, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 131
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037502 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037502
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037502/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037502
Building REAL300000037503
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037503'
/scratch/stefan/7769618/working/building/REAL300000037503 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037503

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037503/0 /scratch/stefan/7769618/working/building/REAL300000037503 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/560
`/scratch/stefan/7769618/working/3D/560' -> `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=CN=CC=N1)

`REAL300000037503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037503 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 158, 159, 106, 106, 106, 106, 106, 106, 106, 106, 106, 40, 8, 40, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 106, 106, 106, 40, 40, 40, 40, 1, 1, 1] 159
rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 325
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: REAL300000037503 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 106, 106, 106, 106, 106, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 106, 106, 106] 159
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 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: 223
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037503 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037503
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037503/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037503
Building REAL300000037504
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037504'
/scratch/stefan/7769618/working/building/REAL300000037504 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037504

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037504/0 /scratch/stefan/7769618/working/building/REAL300000037504 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/561
`/scratch/stefan/7769618/working/3D/561' -> `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=CN=CC=N3)C=C2)C=C1)

`REAL300000037504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037504 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 1, 1, 1, 1, 1, 1, 6, 30, 31, 57, 57, 57, 57, 57, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 57, 57, 57, 1, 1, 3, 3] 68
rigid atoms, others: [34, 33, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037504 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 59, 68, 57, 68, 68, 57, 38, 57, 57, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 57, 57, 68, 68, 68, 68, 57, 57, 28, 28, 1, 1, 1, 57, 57, 68, 68] 68
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 315
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037504 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 2, 13, 48, 48, 68, 68, 68, 68, 68, 3, 3, 1, 1, 1, 1, 3, 3, 13, 13, 68, 68, 68, 3, 3, 1, 1] 68
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037504 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037504
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037504/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037504
Building REAL300000037505
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037505'
/scratch/stefan/7769618/working/building/REAL300000037505 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037505

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037505/0 /scratch/stefan/7769618/working/building/REAL300000037505 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/562
`/scratch/stefan/7769618/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CN=CC=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037505 none COC1=CC(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 114, 113, 113, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 113, 113, 114, 113, 113, 190, 201, 201, 201, 201, 141, 141, 141, 113, 23, 23, 1, 1, 1, 113, 201, 201, 201, 201] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37])
total number of confs: 419
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037505 none COC1=CC(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 64, 65, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 3, 3, 3, 1, 8, 8, 114, 114, 114, 1, 7, 7, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037505 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037505/1 /scratch/stefan/7769618/working/building/REAL300000037505 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/563
`/scratch/stefan/7769618/working/3D/563' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CN=CC=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000037505.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037505/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037505 none COC1=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [57, 32, 32, 32, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 65, 89, 89, 95, 95, 57, 57, 57, 32, 11, 4, 1, 1, 1, 32, 89, 89, 89, 89] 95
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37])
total number of confs: 282
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037505 none COC1=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 27, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 4, 4, 4, 1, 8, 27, 32, 32, 32, 1, 14, 14, 14, 14] 95
rigid atoms, others: [1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 157
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037505 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037505
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037505/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037505/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037505
Building REAL300000037506
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037506'
/scratch/stefan/7769618/working/building/REAL300000037506 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037506

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037506/0 /scratch/stefan/7769618/working/building/REAL300000037506 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/564
`/scratch/stefan/7769618/working/3D/564' -> `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=CN=CC=N3)O2)=CC=C1O)

`REAL300000037506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037506 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [9, 8, 9, 8, 8, 1, 1, 1, 1, 1, 1, 8, 68, 68, 127, 127, 127, 127, 127, 1, 8, 8, 8, 8, 8, 1, 1, 8, 8, 127, 127, 127, 8, 8, 16] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037506 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 127, 127, 127, 127, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 127, 201, 201, 201, 201, 201, 127, 127, 30, 30, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 739
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037506 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CN=CC=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 8, 8, 8, 8, 47, 159, 159, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 8, 8, 47, 47, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037506 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037506
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037506/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037506
Building REAL300000037507
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037507'
/scratch/stefan/7769618/working/building/REAL300000037507 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037507

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037507/0 /scratch/stefan/7769618/working/building/REAL300000037507 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/565
`/scratch/stefan/7769618/working/3D/565' -> `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=CN=CC=N3)S2)C=C1)

`REAL300000037507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 63, 63, 103, 103, 103, 103, 103, 1, 7, 7, 7, 7, 1, 1, 8, 8, 103, 103, 103, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 128, 201, 201, 103, 103, 103, 103, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 103, 103, 37, 37, 1, 1, 1, 201, 201] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 629
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 162, 162, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 9, 9, 36, 36, 201, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037507 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037507/1 /scratch/stefan/7769618/working/building/REAL300000037507 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/566
`/scratch/stefan/7769618/working/3D/566' -> `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=CN=CC=N3)S2)C=C1)

`REAL300000037507.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037507/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 10, 12, 12, 12, 12, 12, 1, 7, 7, 7, 7, 1, 1, 6, 10, 12, 12, 12, 7, 7] 30
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [30, 30, 30, 14, 30, 30, 12, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 12, 12, 6, 2, 1, 1, 1, 30, 30] 30
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 110
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037507 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CN=CC=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 8, 8, 24, 28, 28, 28, 28, 1, 1] 28
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037507 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037507
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037507/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037507/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037507
Building REAL300000037508
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037508'
/scratch/stefan/7769618/working/building/REAL300000037508 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037508

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037508/0 /scratch/stefan/7769618/working/building/REAL300000037508 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/567
`/scratch/stefan/7769618/working/3D/567' -> `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=CN=CC=N3)S2)=C1)

`REAL300000037508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 9, 60, 60, 102, 102, 102, 102, 102, 1, 11, 11, 11, 11, 1, 1, 9, 9, 102, 102, 102, 11] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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, 201, 102, 102, 102, 102, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 102, 102, 24, 24, 1, 1, 1, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 321
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 56, 169, 169, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 11, 11, 56, 56, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037508 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037508/1 /scratch/stefan/7769618/working/building/REAL300000037508 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/568
`/scratch/stefan/7769618/working/3D/568' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CN=CC=N3)S2)=C1)

`REAL300000037508.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037508/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 27, 30, 30, 30, 30, 30, 1, 13, 12, 13, 13, 1, 1, 6, 27, 30, 30, 30, 13] 60
rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 30, 30, 30, 30, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 30, 60, 60, 60, 60, 30, 30, 12, 4, 1, 1, 1, 60] 60
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 92
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037508 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CN=CC=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 44, 44, 60, 60, 60, 60, 60, 60, 13, 1, 1, 1, 1, 13, 13, 44, 60, 60, 60, 60, 1] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037508 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037508
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037508/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037508/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037508
Building REAL300000037509
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037509'
/scratch/stefan/7769618/working/building/REAL300000037509 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037509

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037509/0 /scratch/stefan/7769618/working/building/REAL300000037509 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/569
`/scratch/stefan/7769618/working/3D/569' -> `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=CN=CC=N2)=C1)

`REAL300000037509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037509 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 4, 1, 1, 1, 18] 18
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
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: REAL300000037509 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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, 8, 8, 18, 18, 18, 18, 18, 18, 1, 1, 1, 8, 18, 18, 18, 18, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037509 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037509/1 /scratch/stefan/7769618/working/building/REAL300000037509 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/570
`/scratch/stefan/7769618/working/3D/570' -> `1.mol2'
Preparing input files

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

`REAL300000037509.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037509/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037509 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 67, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 27, 27, 1, 1, 1, 67] 67
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037509 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 52, 52, 67, 67, 67, 67, 67, 1, 1, 1, 8, 8, 67, 67, 67, 1] 67
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037509 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037509
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037509/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037509/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037509
Building REAL300000037510
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037510'
/scratch/stefan/7769618/working/building/REAL300000037510 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037510

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037510/0 /scratch/stefan/7769618/working/building/REAL300000037510 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/571
`/scratch/stefan/7769618/working/3D/571' -> `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=CN=CC=N2)=C1)

`REAL300000037510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037510 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 24, 8, 3, 1, 1, 1, 12] 24
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 27])
total number of confs: 44
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: REAL300000037510 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 8, 8, 12, 12, 12, 12, 12, 12, 1, 1, 2, 8, 12, 12, 12, 12, 1] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 35
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037510 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037510/1 /scratch/stefan/7769618/working/building/REAL300000037510 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/572
`/scratch/stefan/7769618/working/3D/572' -> `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=CN=CC=N2)=C1)

`REAL300000037510.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037510/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037510 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 6, 6, 6, 2, 1, 1, 1, 6] 6
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 26])
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: REAL300000037510 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CN=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 1, 1, 4, 6, 6, 6, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 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/7769618/working/building/REAL300000037510 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037510
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037510/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037510/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037510
Building REAL300000037511
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037511'
/scratch/stefan/7769618/working/building/REAL300000037511 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037511

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037511/0 /scratch/stefan/7769618/working/building/REAL300000037511 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/573
`/scratch/stefan/7769618/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(CN=NC2=CN=CC=N2)=C1OCC(=O)[O-])

`REAL300000037511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037511 none COC1=CC(Br)=CC(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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: [140, 88, 88, 88, 88, 88, 88, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 88, 88, 133, 197, 201, 201, 140, 140, 140, 88, 88, 34, 34, 1, 1, 1, 197, 197] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 30, 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, 33, 34])
total number of confs: 725
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: REAL300000037511 none COC1=CC(Br)=CC(CN=NC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 44, 44, 88, 88, 88, 88, 88, 1, 1, 2, 10, 23, 23, 3, 3, 3, 1, 1, 8, 8, 88, 88, 88, 10, 10] 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])
total number of confs: 222
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037511 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037511/1 /scratch/stefan/7769618/working/building/REAL300000037511 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/574
`/scratch/stefan/7769618/working/3D/574' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(C=NNC2=CN=CC=N2)=C1OCC(=O)[O-])

`REAL300000037511.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037511/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037511 none COC1=CC(Br)=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [24, 16, 16, 16, 16, 16, 16, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 21, 33, 35, 35, 24, 24, 24, 16, 16, 10, 4, 1, 1, 1, 33, 33] 35
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 30, 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, 33, 34])
total number of confs: 112
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: REAL300000037511 none COC1=CC(Br)=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 16, 16, 16, 16, 16, 1, 1, 3, 11, 21, 21, 4, 4, 4, 1, 1, 4, 12, 16, 16, 16, 11, 11] 35
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])
total number of confs: 108
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037511 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037511
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037511/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037511/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037511
Building REAL300000037512
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037512'
/scratch/stefan/7769618/working/building/REAL300000037512 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037512

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037512/0 /scratch/stefan/7769618/working/building/REAL300000037512 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/575
`/scratch/stefan/7769618/working/3D/575' -> `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=CN=CC=N3)C=C2)O1)

`REAL300000037512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037512 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [9, 8, 9, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 63, 63, 117, 117, 117, 117, 117, 1, 1, 8, 8, 8, 1, 1, 1, 1, 9, 9, 117, 117, 117, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 31, 32, 33, 34, 35])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037512 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 117, 117, 51, 27, 117, 117, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 117, 117, 117, 117, 27, 27, 1, 1, 1, 117, 117] 201
rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 616
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037512 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CN=CC=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 8, 8, 8, 8, 8, 8, 52, 167, 167, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 8, 8, 8, 8, 52, 52, 201, 201, 201, 8, 8] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 410
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037512 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037512
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037512/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037512
Building REAL300000037513
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037513'
/scratch/stefan/7769618/working/building/REAL300000037513 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037513

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037513/0 /scratch/stefan/7769618/working/building/REAL300000037513 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/576
`/scratch/stefan/7769618/working/3D/576' -> `0.mol2'
Preparing input files

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

`REAL300000037513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037513 none O=C([O-])C1=CC(I)=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 9, 9, 9, 6, 2, 1, 1, 1, 9] 9
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037513 none O=C([O-])C1=CC(I)=CC(C=NNC2=CN=CC=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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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, 1, 1, 1, 6, 8, 9, 9, 9, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 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/7769618/working/building/REAL300000037513 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037513/1 /scratch/stefan/7769618/working/building/REAL300000037513 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/577
`/scratch/stefan/7769618/working/3D/577' -> `1.mol2'
Preparing input files

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

`REAL300000037513.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037513/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037513 none O=C([O-])C1=CC(I)=CC(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 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, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 27, 27, 1, 1, 1, 86] 86
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26])
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: REAL300000037513 none O=C([O-])C1=CC(I)=CC(CN=NC2=CN=CC=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 86, 86, 86, 86, 86, 1, 1, 1, 9, 9, 86, 86, 86, 1] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037513 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037513
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037513/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037513/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037513
Building REAL300000037514
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037514'
/scratch/stefan/7769618/working/building/REAL300000037514 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037514

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037514/0 /scratch/stefan/7769618/working/building/REAL300000037514 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/578
`/scratch/stefan/7769618/working/3D/578' -> `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=CN=CC=N2)=C1O)

`REAL300000037514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037514 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CN=CC=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 4, 1, 1, 1, 34] 34
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037514 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CN=CC=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 8, 16, 17, 17, 17, 2] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 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/7769618/working/building/REAL300000037514 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037514
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037514/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037514
Building REAL300000037515
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037515'
/scratch/stefan/7769618/working/building/REAL300000037515 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037515

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037515/0 /scratch/stefan/7769618/working/building/REAL300000037515 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/579
`/scratch/stefan/7769618/working/3D/579' -> `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=CN=CC=N3)C=C2)=C1)

`REAL300000037515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037515 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 56, 57, 99, 99, 99, 99, 99, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 99, 99, 99, 1, 1, 3] 201
rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 13, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037515 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 167, 167, 166, 167, 167, 42, 23, 99, 99, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 99, 99, 167, 201, 201, 167, 167, 167, 99, 99, 22, 22, 1, 1, 1, 99, 99, 167] 201
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 688
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037515 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CN=CC=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 103, 103, 167, 167, 167, 167, 167, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 167, 167, 167, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037515 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037515
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037515/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037515
Building REAL300000037516
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037516'
/scratch/stefan/7769618/working/building/REAL300000037516 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037516

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037516/0 /scratch/stefan/7769618/working/building/REAL300000037516 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/580
`/scratch/stefan/7769618/working/3D/580' -> `0.mol2'
Preparing input files

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

`REAL300000037516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037516 none CCOC1=CC(CN=NC2=CN=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [82, 82, 48, 48, 48, 13, 2, 2, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 171, 200, 200, 200, 82, 82, 82, 82, 82, 48, 13, 13, 1, 1, 1, 48, 48, 200, 200] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 31] 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, 34, 35, 36, 37])
total number of confs: 492
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037516 none CCOC1=CC(CN=NC2=CN=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 3, 1, 1, 1, 1, 1, 6, 36, 36, 48, 48, 48, 48, 48, 1, 1, 1, 1, 7, 15, 16, 16, 3, 3, 3, 3, 3, 1, 6, 6, 48, 48, 48, 1, 1, 15, 15] 201
rigid atoms, others: [2, 3, 4, 5, 6, 34, 15, 16, 17, 18, 35, 28] 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, 36, 37])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037516 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037516
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037516/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037516
Building REAL300000037517
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037517'
/scratch/stefan/7769618/working/building/REAL300000037517 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037517

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037517/0 /scratch/stefan/7769618/working/building/REAL300000037517 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/581
`/scratch/stefan/7769618/working/3D/581' -> `0.mol2'
Preparing input files

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

`REAL300000037517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [14, 10, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 31, 31, 31, 31] 31
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 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, 32, 33, 34, 35, 36, 37])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [13, 12, 13, 12, 12, 12, 12, 31, 31, 31, 31, 31, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 8, 2, 1, 1, 1] 31
rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 72
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 4, 12, 12, 12, 12] 31
rigid atoms, others: [32, 1, 3, 4, 5, 6, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037517 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037517/1 /scratch/stefan/7769618/working/building/REAL300000037517 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/582
`/scratch/stefan/7769618/working/3D/582' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC=N1)

`REAL300000037517.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037517/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [9, 7, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 159, 159, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 201, 201, 201] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 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, 32, 33, 34, 35, 36, 37])
total number of confs: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [81, 69, 81, 69, 69, 69, 69, 201, 201, 201, 201, 201, 69, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 24, 24, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 545
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037517 none O=C([O-])C1=NN(C2CCOCC2)C=C1CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 8, 46, 46, 69, 69, 69, 69, 69, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 8, 8, 69, 69, 69] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037517 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037517
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037517/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037517/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037517
Building REAL300000037518
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037518'
/scratch/stefan/7769618/working/building/REAL300000037518 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037518

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037518/0 /scratch/stefan/7769618/working/building/REAL300000037518 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/583
`/scratch/stefan/7769618/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC=N2)=C1C(=O)[O-])

`REAL300000037518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037518 none CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 2, 2, 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: [92, 92, 92, 92, 92, 92, 92, 92, 92, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 92, 92, 93, 93, 93, 93, 93, 92, 92, 92, 41, 41, 1, 1, 1] 93
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037518 none CN1C2=CC=C(F)C=C2C(CN=NC2=CN=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 92, 92, 92, 92, 92, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 7, 7, 92, 92, 92] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 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/7769618/working/building/REAL300000037518 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037518/1 /scratch/stefan/7769618/working/building/REAL300000037518 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/584
`/scratch/stefan/7769618/working/3D/584' -> `1.mol2'
Preparing input files

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

`REAL300000037518.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037518/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037518 none CN1C2=CC=C(F)C=C2C(C=NNC2=CN=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 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, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 1, 1, 1] 9
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 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: REAL300000037518 none CN1C2=CC=C(F)C=C2C(C=NNC2=CN=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 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, 4, 4, 8, 9, 9, 9, 9, 9, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 8, 9, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037518 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037518
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037518/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037518/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037518
Building REAL300000037519
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037519'
/scratch/stefan/7769618/working/building/REAL300000037519 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037519

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037519/0 /scratch/stefan/7769618/working/building/REAL300000037519 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/585
`/scratch/stefan/7769618/working/3D/585' -> `0.mol2'
Preparing input files

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

`REAL300000037519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037519 none CC(N=NC1=CN=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 38, 38, 69, 69, 69, 69, 69, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 69, 69, 69, 1, 1, 1, 1] 69
rigid atoms, others: [32, 1, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037519 none CC(N=NC1=CN=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 35, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 35, 35, 35, 35, 1, 1, 1, 69, 69, 69, 69] 69
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037519 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037519
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037519/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037519
Building REAL300000037520
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037520'
/scratch/stefan/7769618/working/building/REAL300000037520 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037520

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037520/0 /scratch/stefan/7769618/working/building/REAL300000037520 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/586
`/scratch/stefan/7769618/working/3D/586' -> `0.mol2'
Preparing input files

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

`REAL300000037520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037520 none O=C([O-])C1=C(C=NNC2=CN=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 6, 2, 1, 1, 1, 8] 8
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 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: REAL300000037520 none O=C([O-])C1=C(C=NNC2=CN=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 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: [3, 1, 3, 1, 1, 1, 3, 3, 7, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 7, 8, 8, 8, 1] 8
rigid atoms, others: [1, 3, 4, 5, 14, 15, 16, 17, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037520 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037520/1 /scratch/stefan/7769618/working/building/REAL300000037520 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/587
`/scratch/stefan/7769618/working/3D/587' -> `1.mol2'
Preparing input files

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

`REAL300000037520.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037520/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037520 none O=C([O-])C1=C(CN=NC2=CN=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 29, 29, 1, 1, 1, 101] 101
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 23])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037520 none O=C([O-])C1=C(CN=NC2=CN=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 8, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 8, 52, 52, 101, 101, 101, 101, 101, 1, 1, 1, 1, 8, 8, 101, 101, 101, 1] 101
rigid atoms, others: [1, 3, 4, 5, 14, 15, 16, 17, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22])
total number of confs: 168
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037520 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037520
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037520/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037520/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037520
Building REAL300000037521
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037521'
/scratch/stefan/7769618/working/building/REAL300000037521 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037521

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037521/0 /scratch/stefan/7769618/working/building/REAL300000037521 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/588
`/scratch/stefan/7769618/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CN=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037521 none CC(N=NC1=CN=CC=N1)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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 16, 16, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 26, 26, 26, 1, 1, 1, 1, 1] 26
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037521 none CC(N=NC1=CN=CC=N1)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', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 22, 22, 22, 1, 1, 1, 26, 26, 26, 26, 26] 26
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 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: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037521 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037521/1 /scratch/stefan/7769618/working/building/REAL300000037521 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/589
`/scratch/stefan/7769618/working/3D/589' -> `1.mol2'
Preparing input files

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

`REAL300000037521.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037521/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037521 none CC(=NNC1=CN=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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, 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, 33, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 35
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037521 none CC(=NNC1=CN=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 3, 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: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 2, 1, 1, 1, 11, 11, 11, 11, 11] 11
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 1, 2, 10, 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: 20
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037521 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037521
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037521/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037521/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037521
Building REAL300000037522
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037522'
/scratch/stefan/7769618/working/building/REAL300000037522 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037522

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037522/0 /scratch/stefan/7769618/working/building/REAL300000037522 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/590
`/scratch/stefan/7769618/working/3D/590' -> `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=CN=CC=N2)O1)

`REAL300000037522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037522 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 3, 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: [61, 61, 61, 61, 61, 61, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 38, 39, 79, 79, 79, 79, 79, 61, 61, 61, 21, 21, 1, 1, 1, 1, 7, 7, 79, 79, 79] 143
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037522 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 143, 143, 133, 111, 79, 79, 79, 54, 79, 79, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 133, 133, 79, 78, 79, 79, 38, 38, 1, 1, 1] 143
rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 463
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037522 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CN=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 38, 61, 61, 43, 61, 61, 61, 77, 133, 133, 143, 143, 143, 143, 143, 1, 1, 1, 8, 8, 61, 61, 61, 61, 77, 77, 143, 143, 143] 143
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 370
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037522 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037522
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037522/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037522
Building REAL300000037523
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037523'
/scratch/stefan/7769618/working/building/REAL300000037523 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037523

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037523/0 /scratch/stefan/7769618/working/building/REAL300000037523 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/591
`/scratch/stefan/7769618/working/3D/591' -> `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=CN=CC=N1)

`REAL300000037523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037523 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 7, 7, 7, 7, 3, 1, 1, 1] 7
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23])
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: REAL300000037523 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 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, 1, 1, 1, 4, 6, 7, 7, 7] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 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/7769618/working/building/REAL300000037523 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037523/1 /scratch/stefan/7769618/working/building/REAL300000037523 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/592
`/scratch/stefan/7769618/working/3D/592' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC=N1)

`REAL300000037523.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037523/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037523 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 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, 3, 7, 7, 3, 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, 60, 60, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 28, 28, 1, 1, 1] 60
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23])
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: REAL300000037523 none O=C([O-])C1=C(Br)C=CC=C1CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 46, 46, 60, 60, 60, 60, 60, 1, 1, 1, 8, 8, 60, 60, 60] 60
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037523 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037523
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037523/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037523/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037523
Building REAL300000037524
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037524'
/scratch/stefan/7769618/working/building/REAL300000037524 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037524

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037524/0 /scratch/stefan/7769618/working/building/REAL300000037524 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/593
`/scratch/stefan/7769618/working/3D/593' -> `0.mol2'
Preparing input files

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

`REAL300000037524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037524 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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: [142, 98, 98, 98, 98, 98, 153, 98, 98, 98, 98, 97, 97, 135, 135, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 98, 153, 153, 153, 98, 98, 42, 42, 1, 1, 1] 175
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 556
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037524 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 46, 46, 97, 97, 97, 97, 97, 2, 2, 2, 1, 4, 4, 4, 1, 1, 6, 6, 97, 97, 97] 175
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 33, 28] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037524 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037524/1 /scratch/stefan/7769618/working/building/REAL300000037524 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/594
`/scratch/stefan/7769618/working/3D/594' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CN=CC=N1)

`REAL300000037524.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037524/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037524 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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, 21, 21, 21, 21, 21, 23, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 21, 23, 23, 23, 21, 21, 12, 4, 1, 1, 1] 23
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300000037524 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CN=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 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, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 19, 21, 21, 21, 21, 21, 2, 2, 2, 1, 3, 3, 3, 1, 1, 7, 19, 21, 21, 21] 23
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 33, 28] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037524 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037524
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037524/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037524/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037524
Building REAL300000037525
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037525'
/scratch/stefan/7769618/working/building/REAL300000037525 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037525

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037525/0 /scratch/stefan/7769618/working/building/REAL300000037525 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/595
`/scratch/stefan/7769618/working/3D/595' -> `0.mol2'
Preparing input files

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

`REAL300000037525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037525 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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, 188, 86, 86, 87, 87, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 201, 201, 87, 87, 18, 18, 1, 1, 1, 87] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 389
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037525 none O=C([O-])COC1=CC=C(CN=NC2=CN=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 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: [27, 21, 27, 7, 1, 1, 1, 1, 1, 1, 8, 49, 49, 87, 87, 87, 87, 87, 1, 1, 1, 21, 21, 1, 1, 8, 8, 87, 87, 87, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037525 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037525/1 /scratch/stefan/7769618/working/building/REAL300000037525 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/596
`/scratch/stefan/7769618/working/3D/596' -> `1.mol2'
Preparing input files

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

`REAL300000037525.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037525/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037525 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 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, 101, 43, 27, 43, 43, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 150, 150, 43, 43, 16, 4, 1, 1, 1, 43] 150
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 469
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: REAL300000037525 none O=C([O-])COC1=CC=C(C=NNC2=CN=CC=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 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: [65, 43, 65, 9, 1, 1, 1, 1, 1, 1, 8, 8, 33, 43, 43, 43, 43, 43, 1, 1, 1, 43, 43, 1, 1, 8, 33, 43, 43, 43, 1] 150
rigid atoms, others: [4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 309
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037525 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037525
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037525/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037525/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037525
Building REAL300000037526
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037526'
/scratch/stefan/7769618/working/building/REAL300000037526 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037526

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037526/0 /scratch/stefan/7769618/working/building/REAL300000037526 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/597
`/scratch/stefan/7769618/working/3D/597' -> `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=CN=CC=N2)C=C1)

`REAL300000037526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037526 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 116, 27, 116, 116, 27, 116, 116, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 115, 116, 201, 201, 201, 116, 116, 26, 26, 1, 1, 1, 115, 116] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 982
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037526 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 1, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 58, 58, 115, 115, 115, 115, 115, 1, 1, 9, 9, 5, 1, 1, 8, 8, 115, 115, 115, 1, 1] 201
rigid atoms, others: [33, 34, 5, 8, 9, 10, 11, 12, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 229
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037526 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037526/1 /scratch/stefan/7769618/working/building/REAL300000037526 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/598
`/scratch/stefan/7769618/working/3D/598' -> `1.mol2'
Preparing input files

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

`REAL300000037526.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037526/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037526 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 21, 11, 7, 11, 11, 4, 11, 11, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 26, 21, 11, 11, 4, 2, 1, 1, 1, 11, 11] 26
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
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: REAL300000037526 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CN=CC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 10, 11, 11, 11, 11, 11, 1, 1, 9, 9, 5, 1, 1, 6, 10, 11, 11, 11, 1, 1] 26
rigid atoms, others: [33, 34, 5, 8, 9, 10, 11, 12, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037526 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037526
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037526/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037526/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037526
Building REAL300000037527
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037527'
/scratch/stefan/7769618/working/building/REAL300000037527 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037527

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037527/0 /scratch/stefan/7769618/working/building/REAL300000037527 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/599
`/scratch/stefan/7769618/working/3D/599' -> `0.mol2'
Preparing input files

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

`REAL300000037527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037527 none O=C([O-])C1=CC2=C(C=NNC3=CN=CC=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 4, 2, 1, 1, 1, 8, 8] 8
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29])
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: REAL300000037527 none O=C([O-])C1=CC2=C(C=NNC3=CN=CC=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 1, 1] 8
rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037527 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037527
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037527/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037527
Building REAL300000037528
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037528'
/scratch/stefan/7769618/working/building/REAL300000037528 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037528

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037528/0 /scratch/stefan/7769618/working/building/REAL300000037528 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/600
`/scratch/stefan/7769618/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)

`REAL300000037528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037528 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 25, 27, 27, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 24, 8, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 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: REAL300000037528 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 6, 16, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037528 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037528
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037528/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037528
Building REAL300000037529
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037529'
/scratch/stefan/7769618/working/building/REAL300000037529 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037529

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037529/0 /scratch/stefan/7769618/working/building/REAL300000037529 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/601
`/scratch/stefan/7769618/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037529 none O=C([O-])COC1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 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, 7, 4, 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, 141, 63, 63, 63, 35, 63, 63, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 63, 63, 63, 63, 35, 11, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 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, 12, 32, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 662
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037529 none O=C([O-])COC1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 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, 7, 4, 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: [58, 36, 58, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 36, 36, 1, 1, 1, 1, 6, 18, 63, 63, 63, 63] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037529 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037529
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037529/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037529
Building REAL300000037530
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037530'
/scratch/stefan/7769618/working/building/REAL300000037530 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037530

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037530/0 /scratch/stefan/7769618/working/building/REAL300000037530 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/602
`/scratch/stefan/7769618/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1OCC(=O)[O-])

`REAL300000037530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037530 none COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens 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, 37, 37, 37, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 129, 199, 201, 201, 64, 64, 64, 37, 10, 4, 1, 1, 1, 1, 37, 37, 199, 199] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 586
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037530 none COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 9, 37, 57, 57, 3, 3, 3, 1, 7, 15, 37, 37, 37, 37, 1, 1, 37, 37] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037530 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037530
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037530/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037530
Building REAL300000037531
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037531'
/scratch/stefan/7769618/working/building/REAL300000037531 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037531

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037531/0 /scratch/stefan/7769618/working/building/REAL300000037531 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/603
`/scratch/stefan/7769618/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)

`REAL300000037531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037531 none O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 109, 32, 32, 68, 68, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 68, 68, 32, 8, 1, 1, 1, 1, 68, 68] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 717
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: REAL300000037531 none O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 15, 32, 3, 1, 1, 1, 1, 1, 1, 8, 8, 28, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 15, 15, 1, 1, 8, 28, 68, 68, 68, 68, 1, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 23, 24, 36, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 225
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037531 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037531
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037531/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037531
Building REAL300000037532
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037532'
/scratch/stefan/7769618/working/building/REAL300000037532 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037532

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037532/0 /scratch/stefan/7769618/working/building/REAL300000037532 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/604
`/scratch/stefan/7769618/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000037532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037532 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 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: [9, 1, 9, 9, 23, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 5, 17, 26, 26, 1, 9, 9, 9, 23, 51, 51, 51, 51, 1, 1, 1, 17, 17, 1] 201
rigid atoms, others: [1, 34, 35, 36, 39, 15, 16, 17, 18, 19, 20, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 188
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: REAL300000037532 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 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: [14, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 51, 51, 51, 51, 51, 138, 201, 201, 201, 51, 15, 15, 15, 5, 1, 1, 1, 1, 51, 51, 51, 201, 201, 51] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 552
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037532 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037532
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037532/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037532
Building REAL300000037533
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037533'
/scratch/stefan/7769618/working/building/REAL300000037533 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037533

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037533/0 /scratch/stefan/7769618/working/building/REAL300000037533 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/605
`/scratch/stefan/7769618/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037533 none O=C([O-])C1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 32, 32, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 32, 11, 1, 1, 1, 1] 44
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037533 none O=C([O-])C1=CC=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 22, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 6, 22, 44, 44, 44, 44] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26] set([0, 32, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037533 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037533
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037533/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037533
Building REAL300000037534
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037534'
/scratch/stefan/7769618/working/building/REAL300000037534 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037534

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037534/0 /scratch/stefan/7769618/working/building/REAL300000037534 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/606
`/scratch/stefan/7769618/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000037534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037534 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [6, 1, 6, 6, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 29, 40, 40, 40, 40, 1, 1, 1, 1] 40
rigid atoms, others: [32, 1, 34, 35, 33, 15, 16, 17, 18, 19, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 90
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: REAL300000037534 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 40, 40, 28, 40, 40, 40, 40, 40, 28, 28, 28, 8, 1, 1, 1, 1, 40, 40, 40, 40] 40
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 35, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 134
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037534 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037534
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037534/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037534
Building REAL300000037535
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037535'
/scratch/stefan/7769618/working/building/REAL300000037535 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037535

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037535/0 /scratch/stefan/7769618/working/building/REAL300000037535 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/607
`/scratch/stefan/7769618/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000037535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037535 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 32, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 32, 78, 78, 78, 78, 1, 1, 2, 2, 1, 1] 94
rigid atoms, others: [1, 34, 37, 38, 33, 15, 16, 17, 18, 19, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 165
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: REAL300000037535 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 78, 78, 47, 65, 94, 94, 94, 78, 78, 38, 38, 38, 12, 1, 1, 1, 1, 78, 78, 94, 94, 78, 78] 94
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 412
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037535 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037535
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037535/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037535
Building REAL300000037536
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037536'
/scratch/stefan/7769618/working/building/REAL300000037536 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037536

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037536/0 /scratch/stefan/7769618/working/building/REAL300000037536 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/608
`/scratch/stefan/7769618/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CCC2)

`REAL300000037536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037536 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 54, 54, 53, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 54, 54, 54, 10, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53] 54
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 82
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: REAL300000037536 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 9, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1] 54
rigid atoms, others: [0, 1, 2, 3, 36, 37, 6, 7, 8, 9, 10, 11, 34, 35, 23, 24, 25, 38, 39] set([32, 33, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 81
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037536 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037536
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037536/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037536
Building REAL300000037537
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037537'
/scratch/stefan/7769618/working/building/REAL300000037537 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037537

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037537/0 /scratch/stefan/7769618/working/building/REAL300000037537 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/609
`/scratch/stefan/7769618/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)

`REAL300000037537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037537 none O=C([O-])CCOC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 181, 125, 29, 29, 73, 73, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 181, 181, 73, 73, 29, 8, 1, 1, 1, 1, 73, 73] 201
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 702
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: REAL300000037537 none O=C([O-])CCOC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 23, 13, 3, 1, 1, 1, 1, 1, 1, 9, 9, 28, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 18, 18, 13, 13, 1, 1, 9, 28, 73, 73, 73, 73, 1, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 39, 24, 25, 38, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 229
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037537 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037537
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037537/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037537
Building REAL300000037538
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037538'
/scratch/stefan/7769618/working/building/REAL300000037538 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037538

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037538/0 /scratch/stefan/7769618/working/building/REAL300000037538 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/610
`/scratch/stefan/7769618/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)C(=O)[O-])

`REAL300000037538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037538 none CC(OC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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, 167, 52, 52, 51, 52, 52, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 201, 51, 52, 52, 19, 8, 1, 1, 1, 1, 52] 201
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 435
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037538 none CC(OC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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: [25, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 25, 34, 34, 25, 25, 25, 25, 1, 1, 1, 7, 18, 52, 52, 52, 52, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 39, 22, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 204
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037538 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037538
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037538/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037538
Building REAL300000037539
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037539'
/scratch/stefan/7769618/working/building/REAL300000037539 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037539

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037539/0 /scratch/stefan/7769618/working/building/REAL300000037539 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/611
`/scratch/stefan/7769618/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037539 none O=C([O-])CCOC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 185, 134, 44, 44, 44, 44, 44, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 201, 201, 185, 185, 44, 44, 44, 19, 9, 1, 1, 1, 1, 44] 201
rigid atoms, others: [35, 36, 37, 38, 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, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 547
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: REAL300000037539 none O=C([O-])CCOC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 36, 20, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 28, 28, 20, 20, 1, 1, 1, 6, 16, 44, 44, 44, 44, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 39, 25, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 235
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037539 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037539
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037539/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037539
Building REAL300000037540
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037540'
/scratch/stefan/7769618/working/building/REAL300000037540 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037540

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037540/0 /scratch/stefan/7769618/working/building/REAL300000037540 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/612
`/scratch/stefan/7769618/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037540 none O=C([O-])COC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 53, 53, 53, 53, 53, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 53, 53, 53, 23, 9, 1, 1, 1, 1, 53] 201
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 36, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 589
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: REAL300000037540 none O=C([O-])COC1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 34, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 18, 18, 1, 1, 1, 8, 22, 53, 53, 53, 53, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 24, 36, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35])
total number of confs: 216
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037540 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037540
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037540/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037540
Building REAL300000037541
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037541'
/scratch/stefan/7769618/working/building/REAL300000037541 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037541

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037541/0 /scratch/stefan/7769618/working/building/REAL300000037541 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/613
`/scratch/stefan/7769618/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(OCC(=O)[O-])=C1)

`REAL300000037541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037541 none COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 36, 21, 36, 36, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 98, 199, 201, 201, 36, 60, 60, 60, 36, 36, 21, 9, 1, 1, 1, 1, 199, 199, 36] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037541 none COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 7, 29, 50, 50, 1, 2, 2, 2, 1, 1, 4, 8, 36, 36, 36, 36, 29, 29, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037541 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037541
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037541/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037541
Building REAL300000037542
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037542'
/scratch/stefan/7769618/working/building/REAL300000037542 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037542

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037542/0 /scratch/stefan/7769618/working/building/REAL300000037542 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/614
`/scratch/stefan/7769618/working/3D/614' -> `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=NS(=O)(=O)C3=CC=CC=C32)C=C1)

`REAL300000037542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037542 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 200, 201, 97, 200, 200, 16, 16, 45, 45, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 16, 6, 1, 1, 1, 1, 45, 45] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 25, 26, 27, 28, 29, 30, 36])
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: REAL300000037542 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [44, 28, 44, 7, 28, 28, 1, 1, 1, 1, 1, 1, 6, 6, 19, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 6, 19, 45, 45, 45, 45, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037542 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037542
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037542/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037542
Building REAL300000037543
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037543'
/scratch/stefan/7769618/working/building/REAL300000037543 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037543

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037543/0 /scratch/stefan/7769618/working/building/REAL300000037543 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/615
`/scratch/stefan/7769618/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)

`REAL300000037543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037543 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 54, 12, 1, 1, 1, 1, 111, 111] 111
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
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: REAL300000037543 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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
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, 1, 2, 2, 1, 1, 1, 1, 12, 12, 50, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 4, 4, 4, 1, 12, 50, 111, 111, 111, 111, 1, 1] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 38, 9, 10, 11, 12, 26, 27, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037543 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037543
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037543/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037543
Building REAL300000037544
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037544'
/scratch/stefan/7769618/working/building/REAL300000037544 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037544

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037544/0 /scratch/stefan/7769618/working/building/REAL300000037544 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/616
`/scratch/stefan/7769618/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)N1)

`REAL300000037544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037544 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 4, 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, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 33, 8, 1, 1, 1, 1, 46] 46
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 30])
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: REAL300000037544 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 7, 30, 46, 46, 46, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037544 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037544
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037544/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037544
Building REAL300000037545
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037545'
/scratch/stefan/7769618/working/building/REAL300000037545 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037545

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037545/0 /scratch/stefan/7769618/working/building/REAL300000037545 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/617
`/scratch/stefan/7769618/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000037545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037545 none CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [18, 7, 1, 7, 7, 28, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 28, 69, 69, 69, 69, 1, 1, 1, 1] 87
rigid atoms, others: [2, 35, 36, 37, 38, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 177
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: REAL300000037545 none CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [65, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 69, 69, 43, 62, 69, 69, 69, 69, 65, 65, 65, 65, 65, 10, 1, 1, 1, 1, 69, 69, 69, 69] 87
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 376
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037545 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037545
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037545/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037545
Building REAL300000037546
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037546'
/scratch/stefan/7769618/working/building/REAL300000037546 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037546

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037546/0 /scratch/stefan/7769618/working/building/REAL300000037546 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/618
`/scratch/stefan/7769618/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC=C1C(=O)[O-])

`REAL300000037546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037546 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 23, 49, 49, 49, 49, 1, 1, 1, 1] 49
rigid atoms, others: [32, 1, 34, 35, 33, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300000037546 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 13, 1, 1, 1, 1, 49, 49, 49, 49] 49
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 35, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 85
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037546 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037546
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037546/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037546
Building REAL300000037547
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037547'
/scratch/stefan/7769618/working/building/REAL300000037547 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037547

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037547/0 /scratch/stefan/7769618/working/building/REAL300000037547 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/619
`/scratch/stefan/7769618/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000037547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037547 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 33, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 33, 61, 61, 61, 61, 1, 1, 1, 2] 122
rigid atoms, others: [1, 34, 35, 33, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 133
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: REAL300000037547 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 61, 61, 61, 61, 61, 61, 61, 61, 61, 29, 29, 29, 8, 1, 1, 1, 1, 61, 61, 61, 122] 122
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 35, 36, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 218
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037547 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037547
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037547/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037547
Building REAL300000037548
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037548'
/scratch/stefan/7769618/working/building/REAL300000037548 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037548

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037548/0 /scratch/stefan/7769618/working/building/REAL300000037548 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/620
`/scratch/stefan/7769618/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000037548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037548 none CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [32, 12, 1, 12, 12, 67, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 32, 32, 32, 32, 32, 67, 160, 160, 160, 160, 1, 1, 1] 189
rigid atoms, others: [2, 36, 37, 38, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 395
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: REAL300000037548 none CCC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [90, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 160, 160, 160, 160, 160, 160, 160, 160, 160, 90, 90, 90, 90, 90, 9, 1, 1, 1, 1, 160, 160, 160] 189
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 433
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037548 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037548
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037548/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037548
Building REAL300000037549
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037549'
/scratch/stefan/7769618/working/building/REAL300000037549 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037549

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037549/0 /scratch/stefan/7769618/working/building/REAL300000037549 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/621
`/scratch/stefan/7769618/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=C2C=C1)

`REAL300000037549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037549 none O=C([O-])C1=CC2=NNC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 42, 42, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 42, 13, 1, 1, 1, 1, 55, 55] 55
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037549 none O=C([O-])C1=CC2=NNC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 10, 32, 55, 55, 55, 55, 1, 1] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 23, 24, 25, 26, 27] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037549 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037549/1 /scratch/stefan/7769618/working/building/REAL300000037549 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/622
`/scratch/stefan/7769618/working/3D/622' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=NNC2=C1)

`REAL300000037549.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037549/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037549 none O=C([O-])C1=CC=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 49, 13, 1, 1, 1, 1, 89, 89] 89
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 22, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037549 none O=C([O-])C1=CC=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 50, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 12, 50, 89, 89, 89, 89, 1, 1] 89
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 186
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037549 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037549
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037549/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037549/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037549
Building REAL300000037550
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037550'
/scratch/stefan/7769618/working/building/REAL300000037550 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037550

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037550/0 /scratch/stefan/7769618/working/building/REAL300000037550 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/623
`/scratch/stefan/7769618/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000037550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037550 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [12, 1, 12, 12, 43, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 43, 68, 68, 68, 68, 1, 1, 1, 1] 68
rigid atoms, others: [32, 1, 34, 35, 33, 15, 16, 17, 18, 19, 20, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 161
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: REAL300000037550 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 68, 68, 68, 68, 68, 68, 68, 68, 36, 36, 36, 10, 1, 1, 1, 1, 68, 68, 68, 68] 68
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 35, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 111
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037550 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037550
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037550/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037550
Building REAL300000037551
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037551'
/scratch/stefan/7769618/working/building/REAL300000037551 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037551

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037551/0 /scratch/stefan/7769618/working/building/REAL300000037551 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/624
`/scratch/stefan/7769618/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)N=N1)

`REAL300000037551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037551 none O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 43, 43, 43, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 63, 63, 43, 29, 8, 1, 1, 1, 1] 63
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037551 none O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 1, 1, 1, 1, 1, 7, 7, 23, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 7, 7, 1, 7, 23, 43, 43, 43, 43] 63
rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 25] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037551 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037551
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037551/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037551
Building REAL300000037552
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037552'
/scratch/stefan/7769618/working/building/REAL300000037552 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037552

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037552/0 /scratch/stefan/7769618/working/building/REAL300000037552 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/625
`/scratch/stefan/7769618/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000037552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037552 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [13, 1, 13, 13, 63, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 63, 113, 113, 113, 113, 1, 1, 1] 113
rigid atoms, others: [1, 34, 35, 33, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 233
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: REAL300000037552 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 113, 113, 113, 113, 113, 113, 113, 113, 113, 43, 43, 43, 8, 1, 1, 1, 1, 113, 113, 113] 113
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 35, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 172
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037552 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037552
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037552/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037552
Building REAL300000037553
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037553'
/scratch/stefan/7769618/working/building/REAL300000037553 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037553

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037553/0 /scratch/stefan/7769618/working/building/REAL300000037553 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/626
`/scratch/stefan/7769618/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037553 none O=C([O-])C1=CSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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, 51, 51, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 30, 8, 1, 1, 1, 1, 51] 51
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 29])
total number of confs: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037553 none O=C([O-])C1=CSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 9, 24, 51, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037553 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037553
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037553/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037553
Building REAL300000037554
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037554'
/scratch/stefan/7769618/working/building/REAL300000037554 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037554

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037554/0 /scratch/stefan/7769618/working/building/REAL300000037554 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/627
`/scratch/stefan/7769618/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(Cl)=C1)

`REAL300000037554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037554 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 37, 41, 41, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 36, 11, 1, 1, 1, 1, 41] 41
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27])
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: REAL300000037554 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 21, 41, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037554 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037554
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037554/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037554
Building REAL300000037555
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037555'
/scratch/stefan/7769618/working/building/REAL300000037555 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037555

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037555/0 /scratch/stefan/7769618/working/building/REAL300000037555 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/628
`/scratch/stefan/7769618/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000037555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037555 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 39, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 39, 95, 95, 95, 95, 1, 2, 2, 2, 2, 2, 2] 95
rigid atoms, others: [1, 34, 15, 16, 17, 18, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
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: REAL300000037555 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [46, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 47, 47, 47, 13, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95] 95
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 152
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037555 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037555
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037555/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037555
Building REAL300000037556
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037556'
/scratch/stefan/7769618/working/building/REAL300000037556 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037556

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037556/0 /scratch/stefan/7769618/working/building/REAL300000037556 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/629
`/scratch/stefan/7769618/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1O)

`REAL300000037556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037556 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 69, 69, 70, 37, 10, 1, 1, 1, 1, 70, 70, 140] 140
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037556 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 11, 35, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 11, 35, 70, 70, 70, 70, 1, 1, 2] 140
rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 146
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037556 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037556
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037556/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037556
Building REAL300000037557
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037557'
/scratch/stefan/7769618/working/building/REAL300000037557 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037557

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037557/0 /scratch/stefan/7769618/working/building/REAL300000037557 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/630
`/scratch/stefan/7769618/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000037557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037557 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 35, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 61, 61, 61, 61, 1, 1, 1, 2, 2, 2] 61
rigid atoms, others: [1, 34, 35, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 135
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037557 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 61, 61, 61, 61, 61, 61, 61, 61, 61, 38, 38, 38, 12, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61] 61
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037557 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037557
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037557/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037557
Building REAL300000037558
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037558'
/scratch/stefan/7769618/working/building/REAL300000037558 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037558

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037558/0 /scratch/stefan/7769618/working/building/REAL300000037558 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/631
`/scratch/stefan/7769618/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])O1)

`REAL300000037558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037558 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [10, 1, 10, 10, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 46, 46, 46, 46, 1, 1] 46
rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037558 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 46, 46, 46, 46, 46, 46, 46, 35, 35, 35, 11, 1, 1, 1, 1, 46, 46] 46
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 75
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037558 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037558
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037558/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037558
Building REAL300000037559
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037559'
/scratch/stefan/7769618/working/building/REAL300000037559 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037559

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037559/0 /scratch/stefan/7769618/working/building/REAL300000037559 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/632
`/scratch/stefan/7769618/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)C(=O)[O-])

`REAL300000037559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037559 none CC(OC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 156, 32, 32, 88, 88, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 199, 201, 201, 199, 199, 199, 199, 88, 88, 32, 8, 1, 1, 1, 1, 88, 88] 201
rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 650
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: REAL300000037559 none CC(OC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 1, 1, 1, 1, 1, 8, 8, 38, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 19, 29, 29, 19, 19, 19, 19, 1, 1, 8, 38, 88, 88, 88, 88, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 262
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037559 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037559
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037559/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037559
Building REAL300000037560
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037560'
/scratch/stefan/7769618/working/building/REAL300000037560 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037560

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037560/0 /scratch/stefan/7769618/working/building/REAL300000037560 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/633
`/scratch/stefan/7769618/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21)

`REAL300000037560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037560 none O=C([O-])C1CCC(=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 1, 1, 1, 1, 30, 30, 30, 30] 30
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 49
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: REAL300000037560 none O=C([O-])C1CCC(=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 1, 1, 1, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39] set([0, 32, 2, 34, 35, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31])
total number of confs: 51
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037560 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037560
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037560/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037560
Building REAL300000037561
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037561'
/scratch/stefan/7769618/working/building/REAL300000037561 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037561

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037561/0 /scratch/stefan/7769618/working/building/REAL300000037561 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/634
`/scratch/stefan/7769618/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21)

`REAL300000037561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037561 none O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 115, 114, 114, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 114, 115, 115, 114, 114, 182, 182, 115, 46, 8, 1, 1, 1, 1, 115, 115, 115, 114] 182
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 549
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037561 none O=C([O-])CN1C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 14, 1, 1, 1, 1, 1, 10, 10, 51, 115, 115, 115, 115, 115, 115, 115, 114, 114, 115, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 50, 115, 115, 114, 114, 1, 1, 1, 1] 182
rigid atoms, others: [3, 4, 5, 6, 7, 39, 25, 21, 22, 23, 24, 36, 26, 38, 29, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037561 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037561
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037561/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037561
Building REAL300000037562
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037562'
/scratch/stefan/7769618/working/building/REAL300000037562 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037562

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037562/0 /scratch/stefan/7769618/working/building/REAL300000037562 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/635
`/scratch/stefan/7769618/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)N1)

`REAL300000037562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037562 none CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 39, 10, 1, 1, 1, 1, 62] 62
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037562 none CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 10, 10, 34, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 2, 2, 2, 1, 10, 34, 62, 62, 62, 62, 1] 62
rigid atoms, others: [0, 1, 2, 3, 33, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037562 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037562
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037562/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037562
Building REAL300000037563
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037563'
/scratch/stefan/7769618/working/building/REAL300000037563 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037563

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037563/0 /scratch/stefan/7769618/working/building/REAL300000037563 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/636
`/scratch/stefan/7769618/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037563 none O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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
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, 50, 51, 51, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 50, 51, 51, 32, 10, 1, 1, 1, 1, 51] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037563 none O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 11, 23, 51, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037563 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037563
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037563/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037563
Building REAL300000037564
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037564'
/scratch/stefan/7769618/working/building/REAL300000037564 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037564

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037564/0 /scratch/stefan/7769618/working/building/REAL300000037564 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/637
`/scratch/stefan/7769618/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000037564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037564 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 30, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 11, 23, 23, 28, 28, 1, 10, 10, 10, 30, 64, 64, 64, 64, 1, 1, 1, 23, 23, 23, 23, 1] 201
rigid atoms, others: [1, 35, 36, 37, 42, 15, 16, 17, 18, 19, 20, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41])
total number of confs: 213
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037564 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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, 7, 7]
0  hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 64, 64, 64, 64, 64, 181, 201, 201, 201, 201, 64, 18, 18, 18, 6, 1, 1, 1, 1, 64, 64, 64, 201, 201, 201, 201, 64] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 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: 372
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037564 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037564
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037564/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037564
Building REAL300000037565
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037565'
/scratch/stefan/7769618/working/building/REAL300000037565 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037565

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037565/0 /scratch/stefan/7769618/working/building/REAL300000037565 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/638
`/scratch/stefan/7769618/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CSC(C(=O)[O-])=C1)

`REAL300000037565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037565 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [10, 1, 10, 10, 36, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 10, 36, 64, 64, 64, 64, 1, 1] 64
rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 139
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037565 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 64, 64, 64, 64, 64, 64, 64, 35, 35, 35, 10, 1, 1, 1, 1, 64, 64] 64
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037565 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037565
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037565/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037565
Building REAL300000037566
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037566'
/scratch/stefan/7769618/working/building/REAL300000037566 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037566

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037566/0 /scratch/stefan/7769618/working/building/REAL300000037566 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/639
`/scratch/stefan/7769618/working/3D/639' -> `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=NS(=O)(=O)C3=CC=CC=C32)C1)

`REAL300000037566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037566 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 6, 1, 1, 1, 1, 1, 6, 6, 6, 49, 49, 49, 49, 6, 6] 49
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 78
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037566 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 38, 49, 38, 38, 49, 49, 45, 49, 49, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 49, 49, 49, 49, 49, 38, 38, 38, 1, 1, 1, 1, 38, 38] 49
rigid atoms, others: [34, 35, 36, 37, 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, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 170
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037566 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 6, 6, 3, 6, 6, 1, 1, 1, 38, 38, 38, 38, 1, 1] 49
rigid atoms, others: [32, 1, 3, 4, 38, 33, 10, 11, 12, 25, 39, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 68
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037566 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037566
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037566/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037566
Building REAL300000037567
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037567'
/scratch/stefan/7769618/working/building/REAL300000037567 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037567

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037567/0 /scratch/stefan/7769618/working/building/REAL300000037567 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/640
`/scratch/stefan/7769618/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NS(=O)(=O)C2=CC=CC=C21)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000037567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037567 none CC(N=NC1=NS(=O)(=O)C2=CC=CC=C21)[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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 7, 14, 14, 1, 1, 1, 4, 4, 4, 4, 48, 48, 48, 48, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 77
rigid atoms, others: [1, 35, 36, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 127
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037567 none CC(N=NC1=NS(=O)(=O)C2=CC=CC=C21)[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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 48, 48, 48, 48, 48, 77, 77, 77, 48, 48, 48, 44, 44, 44, 44, 1, 1, 1, 1, 48, 48, 77, 77, 48, 48, 48, 48, 48, 48] 77
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 310
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037567 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037567
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037567/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037567
Building REAL300000037568
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037568'
/scratch/stefan/7769618/working/building/REAL300000037568 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037568

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037568/0 /scratch/stefan/7769618/working/building/REAL300000037568 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/641
`/scratch/stefan/7769618/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037568 none CC(CCCCCCC(=O)[O-])=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 61, 69, 96, 111, 123, 201, 201, 201, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 61, 61, 73, 73, 94, 94, 115, 115, 127, 127, 199, 199, 4, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 960
number of broken/clashed sets: 125
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037568 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037568
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037568/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037568
Building REAL300000037569
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037569'
/scratch/stefan/7769618/working/building/REAL300000037569 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037569

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037569/0 /scratch/stefan/7769618/working/building/REAL300000037569 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/642
`/scratch/stefan/7769618/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037569 none CC1C(CC(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 83, 83, 83, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 48, 55, 83, 83, 55, 55, 55, 55, 55, 1, 1, 1, 1] 83
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037569 none CC1C(CC(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 15, 15, 1, 1, 1, 1, 13, 13, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 55, 55, 55, 55] 83
rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 34, 26, 27, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 35, 36, 37, 38])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037569 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037569
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037569/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037569
Building REAL300000037570
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037570'
/scratch/stefan/7769618/working/building/REAL300000037570 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037570

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037570/0 /scratch/stefan/7769618/working/building/REAL300000037570 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/643
`/scratch/stefan/7769618/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CS1)

`REAL300000037570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037570 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 51, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 75, 75, 75, 75, 1, 1] 75
rigid atoms, others: [32, 1, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 163
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037570 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 75, 75, 75, 75, 75, 75, 75, 37, 37, 37, 8, 1, 1, 1, 1, 75, 75] 75
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 118
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037570 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037570
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037570/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037570
Building REAL300000037571
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037571'
/scratch/stefan/7769618/working/building/REAL300000037571 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037571

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037571/0 /scratch/stefan/7769618/working/building/REAL300000037571 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/644
`/scratch/stefan/7769618/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC(C(=O)[O-])C1(C)C)

`REAL300000037571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037571 none CC1C(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 48
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037571 none CC1C(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 23
rigid atoms, others: [0, 1, 2, 3, 36, 37, 19, 39, 40, 41, 34, 16, 17, 18, 35, 22, 23, 24, 38, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 25, 26, 27, 30, 31, 32, 33, 42, 43, 44])
total number of confs: 50
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037571 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037571
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037571/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037571
Building REAL300000037572
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037572'
/scratch/stefan/7769618/working/building/REAL300000037572 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037572

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037572/0 /scratch/stefan/7769618/working/building/REAL300000037572 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/645
`/scratch/stefan/7769618/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037572 none CC1CC(C(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 23
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 56
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: REAL300000037572 none CC1CC(C(=O)[O-])CCC1N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 3, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 23
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 34, 32, 26, 27, 28, 29, 30, 31] set([35, 36, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 37])
total number of confs: 41
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037572 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037572
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037572/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037572
Building REAL300000037573
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037573'
/scratch/stefan/7769618/working/building/REAL300000037573 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037573

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037573/0 /scratch/stefan/7769618/working/building/REAL300000037573 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/646
`/scratch/stefan/7769618/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC1C(=O)[O-])

`REAL300000037573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037573 none CC1CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 15] 15
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 30
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037573 none CC1CC(N=NC2=NS(=O)(=O)C3=CC=CC=C32)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 38, 34, 17, 18, 19, 20, 36, 26, 27, 28, 29] set([32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037573 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037573
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037573/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037573
Building REAL300000037574
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037574'
/scratch/stefan/7769618/working/building/REAL300000037574 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037574

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037574/0 /scratch/stefan/7769618/working/building/REAL300000037574 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/647
`/scratch/stefan/7769618/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037574 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 29, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 1, 1, 1, 1] 29
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 48
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: REAL300000037574 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29] 29
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] set([35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 39
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037574 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037574
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037574/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037574
Building REAL300000037575
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037575'
/scratch/stefan/7769618/working/building/REAL300000037575 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037575

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037575/0 /scratch/stefan/7769618/working/building/REAL300000037575 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/648
`/scratch/stefan/7769618/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CN1)

`REAL300000037575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037575 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 39, 9, 1, 1, 1, 1, 49, 49] 49
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 29, 30])
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: REAL300000037575 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 6, 6, 24, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 6, 24, 49, 49, 49, 49, 1, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037575 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037575
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037575/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037575
Building REAL300000037576
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037576'
/scratch/stefan/7769618/working/building/REAL300000037576 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037576

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037576/0 /scratch/stefan/7769618/working/building/REAL300000037576 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/649
`/scratch/stefan/7769618/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037576 none CC(CC1(C(=O)[O-])CCC1)N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 6, 10, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 12
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300000037576 none CC(CC1(C(=O)[O-])CCC1)N=NC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 8, 14, 11, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 4, 1, 1, 1, 2, 2, 1, 1, 1, 5, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 12
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037576 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037576
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037576/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037576
Building REAL300000037577
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037577'
/scratch/stefan/7769618/working/building/REAL300000037577 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037577

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037577/0 /scratch/stefan/7769618/working/building/REAL300000037577 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/650
`/scratch/stefan/7769618/working/3D/650' -> `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=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037577 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 28, 6, 1, 1, 1, 1] 47
rigid atoms, others: [35, 36, 37, 38, 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, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300000037577 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 10, 10, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 1, 2, 2, 2, 1, 10, 32, 47, 47, 47, 47] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037577 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037577
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037577/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037577
Building REAL300000037578
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037578'
/scratch/stefan/7769618/working/building/REAL300000037578 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037578

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037578/0 /scratch/stefan/7769618/working/building/REAL300000037578 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/651
`/scratch/stefan/7769618/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1Cl)

`REAL300000037578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037578 none O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 36, 11, 1, 1, 1, 1] 44
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037578 none O=C([O-])C1=CC=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 8, 24, 44, 44, 44, 44] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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/7769618/working/building/REAL300000037578 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037578
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037578/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037578
Building REAL300000037579
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037579'
/scratch/stefan/7769618/working/building/REAL300000037579 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037579

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037579/0 /scratch/stefan/7769618/working/building/REAL300000037579 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/652
`/scratch/stefan/7769618/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037579 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 1, 1, 1, 1] 28
rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037579 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 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/7769618/working/building/REAL300000037579 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037579
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037579/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037579
Building REAL300000037580
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037580'
/scratch/stefan/7769618/working/building/REAL300000037580 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037580

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037580/0 /scratch/stefan/7769618/working/building/REAL300000037580 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/653
`/scratch/stefan/7769618/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037580 none CN1N=CC(C(=O)[O-])=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 33, 11, 1, 1, 1, 1] 34
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28])
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: REAL300000037580 none CN1N=CC(C(=O)[O-])=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 4, 20, 34, 34, 34, 34] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 26] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037580 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037580
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037580/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037580
Building REAL300000037581
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037581'
/scratch/stefan/7769618/working/building/REAL300000037581 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037581

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037581/0 /scratch/stefan/7769618/working/building/REAL300000037581 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/654
`/scratch/stefan/7769618/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1F)

`REAL300000037581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037581 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [79, 78, 79, 78, 78, 78, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 38, 10, 1, 1, 1, 1, 78] 79
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27])
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: REAL300000037581 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 12, 12, 36, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 12, 36, 78, 78, 78, 78, 1] 79
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 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/7769618/working/building/REAL300000037581 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037581
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037581/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037581
Building REAL300000037582
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037582'
/scratch/stefan/7769618/working/building/REAL300000037582 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037582

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037582/0 /scratch/stefan/7769618/working/building/REAL300000037582 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/655
`/scratch/stefan/7769618/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1)

`REAL300000037582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037582 none O=C([O-])C=CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 138, 80, 80, 80, 80, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 138, 138, 80, 80, 36, 8, 1, 1, 1, 1] 138
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29])
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: REAL300000037582 none O=C([O-])C=CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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: [23, 12, 24, 12, 1, 1, 1, 1, 1, 1, 8, 8, 31, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 12, 12, 1, 1, 8, 31, 80, 80, 80, 80] 138
rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 199
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037582 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037582
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037582/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037582
Building REAL300000037583
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037583'
/scratch/stefan/7769618/working/building/REAL300000037583 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037583

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037583/0 /scratch/stefan/7769618/working/building/REAL300000037583 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/656
`/scratch/stefan/7769618/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CC2)

`REAL300000037583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037583 none O=C([O-])C1=CC=CC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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
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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 15, 15] 15
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 35, 23, 24, 25, 26, 27, 28, 36])
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: REAL300000037583 none O=C([O-])C1=CC=CC2=C1C(=NNC1=NS(=O)(=O)C3=CC=CC=C31)CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 1, 1, 1, 1] 15
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 35, 23, 24, 25, 26, 27, 36] set([0, 32, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/7769618/working/building/REAL300000037583 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037583
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037583/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037583
Building REAL300000037584
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037584'
/scratch/stefan/7769618/working/building/REAL300000037584 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037584

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037584/0 /scratch/stefan/7769618/working/building/REAL300000037584 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/657
`/scratch/stefan/7769618/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000037584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037584 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [12, 1, 12, 12, 45, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 45, 72, 72, 72, 72, 1, 1, 1] 72
rigid atoms, others: [32, 1, 34, 33, 15, 16, 17, 18, 19, 20, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 168
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: REAL300000037584 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 72, 72, 72, 72, 72, 72, 72, 72, 36, 36, 36, 10, 1, 1, 1, 1, 72, 72, 72] 72
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 117
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037584 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037584
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037584/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037584
Building REAL300000037585
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037585'
/scratch/stefan/7769618/working/building/REAL300000037585 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037585

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037585/0 /scratch/stefan/7769618/working/building/REAL300000037585 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/658
`/scratch/stefan/7769618/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1)

`REAL300000037585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037585 none O=C([O-])C1=CC=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 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
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, 62, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 41, 10, 1, 1, 1, 1, 62] 62
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 36, 24, 25, 26, 27, 28, 29, 30, 31])
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: REAL300000037585 none O=C([O-])C1=CC=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 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
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, 1, 8, 8, 34, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 8, 34, 62, 62, 62, 62, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037585 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037585
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037585/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037585
Building REAL300000037586
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037586'
/scratch/stefan/7769618/working/building/REAL300000037586 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037586

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037586/0 /scratch/stefan/7769618/working/building/REAL300000037586 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/659
`/scratch/stefan/7769618/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=N1)

`REAL300000037586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037586 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 57, 58, 57, 57, 57, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 29, 10, 1, 1, 1, 1, 57] 58
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 31])
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: REAL300000037586 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 30, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 10, 30, 57, 57, 57, 57, 1] 58
rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037586 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037586
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037586/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037586
Building REAL300000037587
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037587'
/scratch/stefan/7769618/working/building/REAL300000037587 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037587

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037587/0 /scratch/stefan/7769618/working/building/REAL300000037587 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/660
`/scratch/stefan/7769618/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1O)

`REAL300000037587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037587 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [62, 61, 62, 61, 61, 61, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 36, 9, 1, 1, 1, 1, 61, 122] 124
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 227
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037587 none O=C([O-])C1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 31, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 10, 31, 61, 61, 61, 61, 1, 2] 124
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 33])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037587 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037587
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037587/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037587
Building REAL300000037588
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037588'
/scratch/stefan/7769618/working/building/REAL300000037588 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037588

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037588/0 /scratch/stefan/7769618/working/building/REAL300000037588 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/661
`/scratch/stefan/7769618/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1C(=O)[O-])

`REAL300000037588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037588 none CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [92, 92, 92, 92, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 93, 93, 93, 93, 93, 92, 92, 42, 10, 1, 1, 1, 1, 92] 93
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037588 none CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 46, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 10, 46, 92, 92, 92, 92, 1] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037588 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037588
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037588/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037588
Building REAL300000037589
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037589'
/scratch/stefan/7769618/working/building/REAL300000037589 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037589

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037589/0 /scratch/stefan/7769618/working/building/REAL300000037589 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/662
`/scratch/stefan/7769618/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037589 none O=C([O-])C1=C(Cl)SC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 51, 10, 1, 1, 1, 1, 118] 118
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 29])
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: REAL300000037589 none O=C([O-])C1=C(Cl)SC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 53, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 11, 53, 118, 118, 118, 118, 1] 118
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037589 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037589
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037589/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037589
Building REAL300000037590
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037590'
/scratch/stefan/7769618/working/building/REAL300000037590 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037590

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037590/0 /scratch/stefan/7769618/working/building/REAL300000037590 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/663
`/scratch/stefan/7769618/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000037590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037590 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 47, 47, 47, 47, 1, 1, 1, 2, 2, 2] 47
rigid atoms, others: [1, 34, 35, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 109
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037590 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 47, 47, 34, 42, 47, 47, 47, 47, 47, 35, 35, 35, 8, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47] 47
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 145
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037590 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037590
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037590/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037590
Building REAL300000037591
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037591'
/scratch/stefan/7769618/working/building/REAL300000037591 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037591

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037591/0 /scratch/stefan/7769618/working/building/REAL300000037591 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/664
`/scratch/stefan/7769618/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037591 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 16, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 50, 62, 62, 62, 35, 35, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 35, 12, 1, 1, 1, 1] 62
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27])
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: REAL300000037591 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 16, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 6, 19, 62, 62, 62, 62] 62
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037591 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037591
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037591/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037591
Building REAL300000037592
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037592'
/scratch/stefan/7769618/working/building/REAL300000037592 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037592

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037592/0 /scratch/stefan/7769618/working/building/REAL300000037592 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/665
`/scratch/stefan/7769618/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037592 none CN1N=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 59, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 59, 46, 12, 1, 1, 1, 1] 60
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037592 none CN1N=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 6, 32, 59, 59, 59, 59] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037592 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037592
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037592/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037592
Building REAL300000037593
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037593'
/scratch/stefan/7769618/working/building/REAL300000037593 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037593

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037593/0 /scratch/stefan/7769618/working/building/REAL300000037593 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/666
`/scratch/stefan/7769618/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037593 none CN1C=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 47, 13, 1, 1, 1, 1] 55
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037593 none CN1C=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 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.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 26, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 6, 26, 55, 55, 55, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 26, 27] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037593 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037593
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037593/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037593
Building REAL300000037594
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037594'
/scratch/stefan/7769618/working/building/REAL300000037594 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037594

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037594/0 /scratch/stefan/7769618/working/building/REAL300000037594 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/667
`/scratch/stefan/7769618/working/3D/667' -> `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=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037594 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 3, 1, 1, 1, 1] 9
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037594 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 6, 9, 9, 9, 9] 9
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 7] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037594 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037594
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037594/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037594
Building REAL300000037595
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037595'
/scratch/stefan/7769618/working/building/REAL300000037595 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037595

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037595/0 /scratch/stefan/7769618/working/building/REAL300000037595 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/668
`/scratch/stefan/7769618/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1)

`REAL300000037595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037595 none CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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: [71, 71, 71, 71, 72, 72, 71, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 72, 72, 72, 71, 38, 8, 1, 1, 1, 1] 72
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037595 none CC1=C(C(=O)[O-])C=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 36, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 2, 2, 2, 1, 8, 36, 71, 71, 71, 71] 72
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037595 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037595
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037595/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037595
Building REAL300000037596
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037596'
/scratch/stefan/7769618/working/building/REAL300000037596 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037596

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037596/0 /scratch/stefan/7769618/working/building/REAL300000037596 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/669
`/scratch/stefan/7769618/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)S1)

`REAL300000037596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037596 none CCC1=CC(C(=O)[O-])=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 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
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 68, 68, 68, 66, 68, 74, 74, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 115, 115, 115, 115, 115, 68, 43, 12, 1, 1, 1, 1] 115
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 401
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037596 none CCC1=CC(C(=O)[O-])=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 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
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 24, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 9, 9, 9, 8, 8, 1, 8, 24, 68, 68, 68, 68] 115
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 23, 29] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 150
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037596 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037596
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037596/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037596
Building REAL300000037597
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037597'
/scratch/stefan/7769618/working/building/REAL300000037597 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037597

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037597/0 /scratch/stefan/7769618/working/building/REAL300000037597 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/670
`/scratch/stefan/7769618/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037597 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 34, 9, 1, 1, 1, 1] 87
rigid atoms, others: [33, 34, 35, 36, 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, 12, 32, 25, 26, 27, 28, 29, 30, 31])
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: REAL300000037597 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 52, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 4, 4, 4, 1, 1, 1, 12, 52, 87, 87, 87, 87] 87
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 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: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037597 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037597
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037597/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037597
Building REAL300000037598
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037598'
/scratch/stefan/7769618/working/building/REAL300000037598 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037598

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037598/0 /scratch/stefan/7769618/working/building/REAL300000037598 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/671
`/scratch/stefan/7769618/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1)

`REAL300000037598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037598 none O=C([O-])C1=CC=C2SC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 66, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 40, 12, 1, 1, 1, 1, 66] 66
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037598 none O=C([O-])C1=CC=C2SC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 10, 34, 66, 66, 66, 66, 1] 66
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 35, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037598 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037598
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037598/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037598
Building REAL300000037599
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037599'
/scratch/stefan/7769618/working/building/REAL300000037599 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037599

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037599/0 /scratch/stefan/7769618/working/building/REAL300000037599 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/672
`/scratch/stefan/7769618/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1)

`REAL300000037599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037599 none O=C([O-])C1=CN=C2CCCC(=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 21] 21
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 36
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: REAL300000037599 none O=C([O-])C1=CN=C2CCCC(=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38] set([33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 33
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037599 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037599
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037599/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037599
Building REAL300000037600
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037600'
/scratch/stefan/7769618/working/building/REAL300000037600 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037600

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037600/0 /scratch/stefan/7769618/working/building/REAL300000037600 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/673
`/scratch/stefan/7769618/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037600 none O=C([O-])C1=COC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 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, 51, 51, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 30, 8, 1, 1, 1, 1, 51] 51
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 29])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037600 none O=C([O-])C1=COC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 7, 23, 51, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037600 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037600
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037600/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037600
Building REAL300000037601
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037601'
/scratch/stefan/7769618/working/building/REAL300000037601 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037601

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037601/0 /scratch/stefan/7769618/working/building/REAL300000037601 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/674
`/scratch/stefan/7769618/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(C(=O)[O-])=C1)

`REAL300000037601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037601 none CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 47, 48, 48, 31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 12, 1, 1, 1, 1, 48] 48
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037601 none CC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 6, 19, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 19, 48, 48, 48, 48, 1] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037601 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037601
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037601/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037601
Building REAL300000037602
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037602'
/scratch/stefan/7769618/working/building/REAL300000037602 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037602

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037602/0 /scratch/stefan/7769618/working/building/REAL300000037602 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/675
`/scratch/stefan/7769618/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1C(=O)[O-])

`REAL300000037602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037602 none COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
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, 141, 141, 141, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 167, 167, 167, 167, 167, 141, 53, 10, 1, 1, 1, 1, 141, 141] 167
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 36, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 360
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037602 none COC1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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]
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: [4, 1, 1, 1, 1, 1, 10, 10, 56, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 10, 55, 141, 141, 141, 141, 1, 1] 167
rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037602 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037602
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037602/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037602
Building REAL300000037603
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037603'
/scratch/stefan/7769618/working/building/REAL300000037603 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037603

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037603/0 /scratch/stefan/7769618/working/building/REAL300000037603 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/676
`/scratch/stefan/7769618/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C(F)=C1)

`REAL300000037603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037603 none O=C([O-])C1=CC(F)=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 30, 8, 1, 1, 1, 1, 34] 34
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
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: REAL300000037603 none O=C([O-])C1=CC(F)=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 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, 1, 7, 7, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 25, 33, 33, 33, 33, 1] 34
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 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/7769618/working/building/REAL300000037603 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037603
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037603/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037603
Building REAL300000037604
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037604'
/scratch/stefan/7769618/working/building/REAL300000037604 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037604

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037604/0 /scratch/stefan/7769618/working/building/REAL300000037604 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/677
`/scratch/stefan/7769618/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037604 none CC1=C(C(=O)[O-])NC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 36, 8, 1, 1, 1, 1, 72] 72
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037604 none CC1=C(C(=O)[O-])NC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 40, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 2, 2, 2, 1, 11, 40, 72, 72, 72, 72, 1] 72
rigid atoms, others: [0, 1, 2, 3, 33, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037604 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037604
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037604/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037604
Building REAL300000037605
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037605'
/scratch/stefan/7769618/working/building/REAL300000037605 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037605

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037605/0 /scratch/stefan/7769618/working/building/REAL300000037605 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/678
`/scratch/stefan/7769618/working/3D/678' -> `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=NS(=O)(=O)C3=CC=CC=C32)=C1O)

`REAL300000037605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037605 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 88, 88, 88, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 43, 10, 1, 1, 1, 1, 176] 176
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 307
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: REAL300000037605 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 1, 1, 11, 11, 47, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 1, 11, 47, 88, 88, 88, 88, 2] 176
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 181
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037605 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037605
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037605/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037605
Building REAL300000037606
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037606'
/scratch/stefan/7769618/working/building/REAL300000037606 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037606

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037606/0 /scratch/stefan/7769618/working/building/REAL300000037606 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/679
`/scratch/stefan/7769618/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)SC(Cl)=C1)

`REAL300000037606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037606 none O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 50, 51, 50, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 12, 1, 1, 1, 1, 50] 51
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 29])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037606 none O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 7, 7, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 7, 23, 50, 50, 50, 50, 1] 51
rigid atoms, others: [1, 3, 4, 5, 19, 20, 21, 22, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037606 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037606
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037606/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037606
Building REAL300000037607
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037607'
/scratch/stefan/7769618/working/building/REAL300000037607 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037607

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037607/0 /scratch/stefan/7769618/working/building/REAL300000037607 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/680
`/scratch/stefan/7769618/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)SC=C1)

`REAL300000037607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037607 none O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 38, 39, 38, 34, 34, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 34, 12, 1, 1, 1, 1, 38, 38] 39
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 28, 29])
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: REAL300000037607 none O=C([O-])C1=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 5, 21, 38, 38, 38, 38, 1, 1] 39
rigid atoms, others: [1, 3, 4, 5, 19, 20, 21, 28, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037607 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037607
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037607/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037607
Building REAL300000037608
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037608'
/scratch/stefan/7769618/working/building/REAL300000037608 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037608

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037608/0 /scratch/stefan/7769618/working/building/REAL300000037608 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/681
`/scratch/stefan/7769618/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=CS1)

`REAL300000037608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037608 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 36, 10, 1, 1, 1, 1, 55] 55
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 29])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037608 none O=C([O-])C1=CC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 9, 25, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 9, 25, 55, 55, 55, 55, 1] 55
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037608 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037608
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037608/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037608
Building REAL300000037609
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037609'
/scratch/stefan/7769618/working/building/REAL300000037609 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037609

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037609/0 /scratch/stefan/7769618/working/building/REAL300000037609 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/682
`/scratch/stefan/7769618/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1C(=O)[O-])

`REAL300000037609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037609 none COC1=CC=C(C)C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 71, 71, 71, 71, 71, 71, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 91, 91, 91, 91, 91, 71, 71, 71, 71, 71, 50, 12, 1, 1, 1, 1] 91
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300000037609 none COC1=CC=C(C)C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 7, 27, 71, 71, 71, 71] 91
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037609 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037609
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037609/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037609
Building REAL300000037610
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037610'
/scratch/stefan/7769618/working/building/REAL300000037610 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037610

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037610/0 /scratch/stefan/7769618/working/building/REAL300000037610 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/683
`/scratch/stefan/7769618/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000037610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037610 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 33, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 81, 81, 81, 81, 1, 1, 1, 1] 81
rigid atoms, others: [1, 35, 36, 37, 38, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300000037610 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 43, 43, 43, 12, 1, 1, 1, 1, 81, 81, 81, 81] 81
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 128
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037610 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037610
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037610/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037610
Building REAL300000037611
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037611'
/scratch/stefan/7769618/working/building/REAL300000037611 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037611

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037611/0 /scratch/stefan/7769618/working/building/REAL300000037611 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/684
`/scratch/stefan/7769618/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1)

`REAL300000037611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037611 none O=C([O-])CCC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 196, 155, 71, 71, 71, 71, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 155, 155, 71, 71, 36, 8, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037611 none O=C([O-])CCC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 19, 24, 9, 1, 1, 1, 1, 1, 1, 6, 6, 28, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 19, 19, 9, 9, 1, 1, 6, 28, 71, 71, 71, 71] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037611 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037611
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037611/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037611
Building REAL300000037612
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037612'
/scratch/stefan/7769618/working/building/REAL300000037612 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037612

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037612/0 /scratch/stefan/7769618/working/building/REAL300000037612 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/685
`/scratch/stefan/7769618/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=CC=C1)

`REAL300000037612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037612 none O=C([O-])C1=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 62, 62, 62, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 63, 63, 63, 62, 63, 37, 8, 1, 1, 1, 1, 63, 63, 63] 63
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 22, 23, 24, 25, 26, 27, 28, 29, 36])
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: REAL300000037612 none O=C([O-])C1=C2NC=C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 36, 63, 63, 63, 63, 63, 63, 63, 62, 62, 63, 1, 1, 1, 1, 1, 1, 10, 35, 63, 63, 62, 62, 1, 1, 1] 63
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 36] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037612 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037612
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037612/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037612
Building REAL300000037613
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037613'
/scratch/stefan/7769618/working/building/REAL300000037613 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037613

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037613/0 /scratch/stefan/7769618/working/building/REAL300000037613 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/686
`/scratch/stefan/7769618/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037613 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 39, 39, 39, 39, 1, 1, 1, 1, 1] 39
rigid atoms, others: [1, 36, 37, 38, 39, 40, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 81
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037613 none CC(=NNC1=NS(=O)(=O)C2=CC=CC=C21)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 31, 31, 31, 12, 1, 1, 1, 1, 39, 39, 39, 39, 39] 39
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40])
total number of confs: 67
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037613 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037613
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037613/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037613
Building REAL300000037614
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037614'
/scratch/stefan/7769618/working/building/REAL300000037614 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037614

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037614/0 /scratch/stefan/7769618/working/building/REAL300000037614 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/687
`/scratch/stefan/7769618/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=CC=C2O1)

`REAL300000037614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037614 none O=C([O-])C1=CC2=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 69, 70, 69, 69, 69, 69, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 70, 69, 42, 10, 1, 1, 1, 1, 69, 69] 70
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037614 none O=C([O-])C1=CC2=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 26, 70, 70, 70, 70, 70, 70, 70, 69, 69, 69, 1, 1, 1, 1, 1, 1, 8, 26, 70, 70, 69, 69, 1, 1] 70
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037614 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037614
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037614/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037614
Building REAL300000037615
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037615'
/scratch/stefan/7769618/working/building/REAL300000037615 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037615

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037615/0 /scratch/stefan/7769618/working/building/REAL300000037615 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/688
`/scratch/stefan/7769618/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=CC=CN12)

`REAL300000037615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037615 none O=C([O-])C1=CN=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 42, 10, 1, 1, 1, 1, 57, 57, 57] 58
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 35, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037615 none O=C([O-])C1=CN=C2C(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 8, 34, 57, 57, 57, 57, 1, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 35, 22, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037615 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037615
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037615/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037615
Building REAL300000037616
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037616'
/scratch/stefan/7769618/working/building/REAL300000037616 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037616

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037616/0 /scratch/stefan/7769618/working/building/REAL300000037616 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/689
`/scratch/stefan/7769618/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037616 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 41, 42, 42, 31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 31, 12, 1, 1, 1, 1] 42
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037616 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 20, 42, 42, 42, 42] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037616 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037616
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037616/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037616
Building REAL300000037617
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037617'
/scratch/stefan/7769618/working/building/REAL300000037617 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037617

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037617/0 /scratch/stefan/7769618/working/building/REAL300000037617 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/690
`/scratch/stefan/7769618/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037617 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 56, 57, 57, 32, 12, 1, 1, 1, 1] 57
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31])
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: REAL300000037617 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 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, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 9, 27, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 9, 27, 57, 57, 57, 57] 57
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037617 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037617
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037617/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037617
Building REAL300000037618
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037618'
/scratch/stefan/7769618/working/building/REAL300000037618 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037618

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037618/0 /scratch/stefan/7769618/working/building/REAL300000037618 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/691
`/scratch/stefan/7769618/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1)

`REAL300000037618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037618 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', '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: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 62, 62, 39, 39, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 39, 12, 1, 1, 1, 1, 62] 62
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 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: REAL300000037618 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', '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: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 17, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 6, 17, 62, 62, 62, 62, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 24, 25, 26] set([32, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037618 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037618
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037618/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037618
Building REAL300000037619
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037619'
/scratch/stefan/7769618/working/building/REAL300000037619 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037619

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037619/0 /scratch/stefan/7769618/working/building/REAL300000037619 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/692
`/scratch/stefan/7769618/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1Cl)

`REAL300000037619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037619 none O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 153, 58, 38, 58, 58, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 201, 201, 58, 58, 24, 6, 1, 1, 1, 1, 58] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 36, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 536
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037619 none O=C([O-])COC1=CC=C(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 35, 53, 7, 1, 1, 1, 1, 1, 1, 10, 10, 30, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 35, 35, 1, 1, 10, 30, 58, 58, 58, 58, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 25, 23, 24, 36, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037619 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037619
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037619/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037619
Building REAL300000037620
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037620'
/scratch/stefan/7769618/working/building/REAL300000037620 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037620

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037620/0 /scratch/stefan/7769618/working/building/REAL300000037620 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/693
`/scratch/stefan/7769618/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=C1C(=O)[O-])

`REAL300000037620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037620 none CC1=NSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 36, 10, 1, 1, 1, 1] 47
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 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: REAL300000037620 none CC1=NSC(C=NNC2=NS(=O)(=O)C3=CC=CC=C32)=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.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 3, 3, 2, 2, 2, 6, 24, 47, 47, 47, 47] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037620 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037620
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037620/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037620
Building REAL300000037621
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037621'
/scratch/stefan/7769618/working/building/REAL300000037621 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037621

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037621/0 /scratch/stefan/7769618/working/building/REAL300000037621 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/694
`/scratch/stefan/7769618/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21)

`REAL300000037621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037621 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 33, 8, 1, 1, 1, 1] 52
rigid atoms, others: [33, 34, 35, 36, 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, 12, 32, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037621 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NS(=O)(=O)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', '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: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 3, 3, 3, 1, 1, 1, 10, 26, 52, 52, 52, 52] 52
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 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: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037621 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037621
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037621/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037621
Building REAL300000037622
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037622'
/scratch/stefan/7769618/working/building/REAL300000037622 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037622

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037622/0 /scratch/stefan/7769618/working/building/REAL300000037622 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/695
`/scratch/stefan/7769618/working/3D/695' -> `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=NS(=O)(=O)C4=CC=CC=C43)=N2)C1)

`REAL300000037622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037622 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 9, 9, 30, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 13, 13, 13, 1, 1, 9, 30, 75, 75, 75, 75, 13, 13] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 206
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037622 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 75, 201, 75, 75, 75, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 75, 75, 37, 9, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 468
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037622 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=NS(=O)(=O)C4=CC=CC=C43)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 54, 54, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 54, 119, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 39, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 439
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037622 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037622
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037622/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037622
Building REAL300000037623
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037623'
/scratch/stefan/7769618/working/building/REAL300000037623 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037623

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037623/0 /scratch/stefan/7769618/working/building/REAL300000037623 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/696
`/scratch/stefan/7769618/working/3D/696' -> `0.mol2'
Preparing input files

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

`REAL300000037623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037623 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 108, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 39, 8, 8, 1, 1, 1, 108, 108] 108
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: 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: REAL300000037623 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
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, 7, 7, 34, 63, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 1, 7, 34, 63, 63, 108, 108, 108, 1, 1] 108
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 30, 31] 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: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037623 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037623
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037623/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037623
Building REAL300000037624
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037624'
/scratch/stefan/7769618/working/building/REAL300000037624 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037624

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037624/0 /scratch/stefan/7769618/working/building/REAL300000037624 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/697
`/scratch/stefan/7769618/working/3D/697' -> `0.mol2'
Preparing input files

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

`REAL300000037624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037624 none O=C([O-])COC1=CC=CC=C1C=NNCC1=CC=C(Cl)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 149, 71, 71, 71, 53, 71, 71, 53, 53, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 71, 71, 71, 71, 53, 29, 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: 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: REAL300000037624 none O=C([O-])COC1=CC=CC=C1C=NNCC1=CC=C(Cl)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [51, 30, 51, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 37, 71, 71, 37, 71, 71, 71, 71, 30, 30, 1, 1, 1, 1, 4, 8, 37, 37, 71, 71, 71] 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: 459
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037624 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037624
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037624/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037624
Building REAL300000037625
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037625'
/scratch/stefan/7769618/working/building/REAL300000037625 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037625

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037625/0 /scratch/stefan/7769618/working/building/REAL300000037625 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/698
`/scratch/stefan/7769618/working/3D/698' -> `0.mol2'
Preparing input files

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

`REAL300000037625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037625 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 139, 79, 45, 93, 93, 45, 45, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 93, 93, 45, 25, 6, 6, 1, 1, 1, 93, 93] 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: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037625 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [17, 9, 17, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 66, 93, 93, 93, 93, 93, 93, 93, 1, 1, 9, 9, 1, 1, 6, 14, 66, 66, 93, 93, 93, 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: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037625 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037625
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037625/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037625
Building REAL300000037626
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037626'
/scratch/stefan/7769618/working/building/REAL300000037626 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037626

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037626/0 /scratch/stefan/7769618/working/building/REAL300000037626 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/699
`/scratch/stefan/7769618/working/3D/699' -> `0.mol2'
Preparing input files

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

`REAL300000037626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037626 none CC(OC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 162, 69, 69, 69, 69, 69, 46, 46, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 46, 24, 6, 6, 1, 1, 1, 69] 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: 485
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037626 none CC(OC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 8, 44, 69, 69, 44, 64, 69, 69, 69, 1, 23, 29, 29, 23, 23, 23, 23, 1, 1, 1, 4, 8, 45, 45, 69, 69, 69, 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: 371
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037626 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037626
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037626/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037626
Building REAL300000037627
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037627'
/scratch/stefan/7769618/working/building/REAL300000037627 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037627

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037627/0 /scratch/stefan/7769618/working/building/REAL300000037627 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/700
`/scratch/stefan/7769618/working/3D/700' -> `0.mol2'
Preparing input files

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

`REAL300000037627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037627 none O=C([O-])CCOC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 201, 199, 167, 64, 64, 64, 64, 64, 33, 33, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 199, 199, 64, 64, 64, 33, 15, 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: 450
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: REAL300000037627 none O=C([O-])CCOC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [25, 18, 25, 17, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 53, 64, 64, 53, 62, 64, 64, 64, 1, 18, 18, 17, 17, 1, 1, 1, 6, 10, 53, 53, 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: 334
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037627 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037627
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037627/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037627
Building REAL300000037628
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037628'
/scratch/stefan/7769618/working/building/REAL300000037628 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037628

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037628/0 /scratch/stefan/7769618/working/building/REAL300000037628 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/701
`/scratch/stefan/7769618/working/3D/701' -> `0.mol2'
Preparing input files

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

`REAL300000037628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037628 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 154, 57, 40, 86, 86, 37, 37, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 201, 201, 86, 86, 37, 19, 5, 5, 1, 1, 1, 86] 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: 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: REAL300000037628 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [22, 18, 22, 7, 1, 1, 1, 1, 1, 1, 7, 7, 14, 70, 86, 86, 70, 86, 86, 86, 86, 1, 1, 1, 2, 2, 18, 18, 1, 1, 7, 14, 70, 70, 86, 86, 86, 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: 414
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037628 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037628
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037628/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037628
Building REAL300000037629
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037629'
/scratch/stefan/7769618/working/building/REAL300000037629 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037629

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037629/0 /scratch/stefan/7769618/working/building/REAL300000037629 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/702
`/scratch/stefan/7769618/working/3D/702' -> `0.mol2'
Preparing input files

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

`REAL300000037629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037629 none O=C([O-])COC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 137, 55, 55, 55, 55, 55, 39, 39, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 55, 55, 55, 39, 25, 6, 6, 1, 1, 1, 55] 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: 560
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037629 none O=C([O-])COC1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [25, 18, 25, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 41, 55, 55, 41, 55, 55, 55, 55, 1, 18, 18, 1, 1, 1, 4, 8, 41, 41, 55, 55, 55, 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: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037629 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037629
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037629/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037629
Building REAL300000037630
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037630'
/scratch/stefan/7769618/working/building/REAL300000037630 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037630

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037630/0 /scratch/stefan/7769618/working/building/REAL300000037630 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/703
`/scratch/stefan/7769618/working/3D/703' -> `0.mol2'
Preparing input files

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

`REAL300000037630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037630 none COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [84, 79, 61, 79, 79, 61, 61, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 138, 201, 201, 201, 79, 84, 84, 84, 79, 79, 61, 31, 6, 6, 1, 1, 1, 201, 201, 79] 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: 680
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037630 none COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 45, 79, 79, 79, 79, 79, 79, 79, 1, 1, 7, 28, 38, 38, 1, 3, 3, 3, 1, 1, 4, 8, 45, 45, 79, 79, 79, 28, 28, 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: 341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037630 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037630
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037630/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037630
Building REAL300000037631
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037631'
/scratch/stefan/7769618/working/building/REAL300000037631 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037631

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037631/0 /scratch/stefan/7769618/working/building/REAL300000037631 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/704
`/scratch/stefan/7769618/working/3D/704' -> `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=C(Cl)C=C2Cl)C=C1)

`REAL300000037631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037631 none O=C([O-])C(F)(F)OC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 120, 201, 201, 47, 28, 54, 54, 28, 28, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 28, 16, 5, 5, 1, 1, 1, 54, 54] 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: 702
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037631 none O=C([O-])C(F)(F)OC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 12, 40, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 6, 12, 40, 40, 54, 54, 54, 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: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037631 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037631
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037631/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037631
Building REAL300000037632
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037632'
/scratch/stefan/7769618/working/building/REAL300000037632 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037632

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037632/0 /scratch/stefan/7769618/working/building/REAL300000037632 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/705
`/scratch/stefan/7769618/working/3D/705' -> `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=C(Cl)C=C2Cl)C=C1)

`REAL300000037632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037632 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=C(Cl)C=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', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 139, 139, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 139, 38, 8, 8, 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: REAL300000037632 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=C(Cl)C=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', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 37, 107, 201, 201, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 8, 37, 107, 107, 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: 519
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037632 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037632
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037632/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037632
Building REAL300000037633
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037633'
/scratch/stefan/7769618/working/building/REAL300000037633 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037633

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037633/0 /scratch/stefan/7769618/working/building/REAL300000037633 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/706
`/scratch/stefan/7769618/working/3D/706' -> `0.mol2'
Preparing input files

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

`REAL300000037633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037633 none O=C([O-])C1=CC2=NNC(C=NNCC3=CC=C(Cl)C=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', '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, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
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, 175, 136, 136, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 136, 40, 8, 8, 1, 1, 1, 175, 175] 175
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: 294
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: REAL300000037633 none O=C([O-])C1=CC2=NNC(C=NNCC3=CC=C(Cl)C=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', '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, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 102, 175, 175, 102, 175, 175, 175, 175, 1, 1, 1, 1, 1, 8, 36, 102, 102, 175, 175, 175, 1, 1] 175
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: 724
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037633 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037633/1 /scratch/stefan/7769618/working/building/REAL300000037633 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/707
`/scratch/stefan/7769618/working/3D/707' -> `1.mol2'
Preparing input files

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

`REAL300000037633.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037633/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037633 none O=C([O-])C1=CC=C2C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 102, 102, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 102, 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: 349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037633 none O=C([O-])C1=CC=C2C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 10, 10, 45, 103, 201, 201, 103, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 45, 103, 103, 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: 853
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037633 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037633
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037633/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037633/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037633
Building REAL300000037634
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037634'
/scratch/stefan/7769618/working/building/REAL300000037634 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037634

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037634/0 /scratch/stefan/7769618/working/building/REAL300000037634 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/708
`/scratch/stefan/7769618/working/3D/708' -> `0.mol2'
Preparing input files

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

`REAL300000037634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037634 none O=C([O-])CN1C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 120, 120, 120, 64, 64, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 120, 64, 28, 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: 640
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037634 none O=C([O-])CN1C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 25, 78, 120, 120, 78, 120, 120, 120, 120, 1, 1, 6, 6, 1, 6, 25, 78, 78, 120, 120, 120] 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: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037634 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037634
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037634/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037634
Building REAL300000037635
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037635'
/scratch/stefan/7769618/working/building/REAL300000037635 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037635

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037635/0 /scratch/stefan/7769618/working/building/REAL300000037635 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/709
`/scratch/stefan/7769618/working/3D/709' -> `0.mol2'
Preparing input files

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

`REAL300000037635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037635 none COC1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [96, 55, 55, 55, 23, 23, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 136, 190, 190, 201, 194, 96, 96, 96, 55, 23, 15, 5, 5, 1, 1, 1, 55, 55, 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: 629
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037635 none COC1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 45, 55, 55, 45, 55, 55, 55, 55, 1, 1, 1, 1, 7, 11, 12, 25, 23, 3, 3, 3, 1, 7, 11, 45, 45, 55, 55, 55, 1, 1, 11, 12, 11, 11] 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: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037635 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037635
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037635/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037635
Building REAL300000037636
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037636'
/scratch/stefan/7769618/working/building/REAL300000037636 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037636

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037636/0 /scratch/stefan/7769618/working/building/REAL300000037636 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/710
`/scratch/stefan/7769618/working/3D/710' -> `0.mol2'
Preparing input files

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

`REAL300000037636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037636 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 155, 155, 155, 131, 131, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 131, 41, 8, 8, 1, 1, 1, 155] 155
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: 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: REAL300000037636 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
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, 12, 12, 49, 87, 155, 155, 87, 155, 155, 155, 155, 1, 1, 1, 1, 1, 12, 49, 87, 87, 155, 155, 155, 1] 155
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: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037636 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037636
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037636/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037636
Building REAL300000037637
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037637'
/scratch/stefan/7769618/working/building/REAL300000037637 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037637

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037637/0 /scratch/stefan/7769618/working/building/REAL300000037637 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/711
`/scratch/stefan/7769618/working/3D/711' -> `0.mol2'
Preparing input files

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

`REAL300000037637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037637 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
350  conformations in input
total number of sets (complete confs): 350
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 97, 97, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 173, 97, 34, 7, 7, 1, 1, 1, 175, 175, 350] 350
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: 660
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037637 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
350  conformations in input
total number of sets (complete confs): 350
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 11, 40, 107, 175, 175, 107, 172, 175, 175, 175, 1, 1, 1, 1, 1, 11, 40, 107, 107, 175, 175, 175, 1, 1, 2] 350
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: 754
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037637 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037637
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037637/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037637
Building REAL300000037638
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037638'
/scratch/stefan/7769618/working/building/REAL300000037638 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037638

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037638/0 /scratch/stefan/7769618/working/building/REAL300000037638 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/712
`/scratch/stefan/7769618/working/3D/712' -> `0.mol2'
Preparing input files

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

`REAL300000037638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037638 none CC(OC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 78, 48, 103, 103, 48, 48, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 103, 103, 48, 29, 6, 6, 1, 1, 1, 103, 103] 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: 704
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037638 none CC(OC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 69, 103, 103, 103, 103, 103, 103, 103, 1, 1, 14, 20, 20, 14, 14, 14, 14, 1, 1, 6, 14, 69, 69, 103, 103, 103, 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: 361
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037638 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037638
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037638/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037638
Building REAL300000037639
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037639'
/scratch/stefan/7769618/working/building/REAL300000037639 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037639

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037639/0 /scratch/stefan/7769618/working/building/REAL300000037639 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/713
`/scratch/stefan/7769618/working/3D/713' -> `0.mol2'
Preparing input files

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

`REAL300000037639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037639 none O=C([O-])CN1C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 119, 119, 119, 59, 59, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 201, 201, 119, 59, 27, 6, 6, 1, 1, 1, 119, 119, 119, 119] 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: 641
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037639 none O=C([O-])CN1C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 82, 119, 119, 81, 118, 119, 119, 119, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 22, 82, 82, 119, 119, 119, 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: 522
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037639 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037639
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037639/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037639
Building REAL300000037640
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037640'
/scratch/stefan/7769618/working/building/REAL300000037640 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037640

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037640/0 /scratch/stefan/7769618/working/building/REAL300000037640 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/714
`/scratch/stefan/7769618/working/3D/714' -> `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=C(Cl)C=C2Cl)N1)

`REAL300000037640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037640 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 160, 160, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 160, 41, 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: 326
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: REAL300000037640 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 6, 6, 32, 109, 201, 201, 109, 200, 201, 201, 201, 1, 2, 2, 2, 1, 6, 32, 109, 109, 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: 843
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037640 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037640
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037640/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037640
Building REAL300000037641
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037641'
/scratch/stefan/7769618/working/building/REAL300000037641 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037641

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037641/0 /scratch/stefan/7769618/working/building/REAL300000037641 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/715
`/scratch/stefan/7769618/working/3D/715' -> `0.mol2'
Preparing input files

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

`REAL300000037641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037641 none O=C([O-])C1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
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, 131, 131, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 131, 41, 8, 8, 1, 1, 1, 184] 184
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: 322
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: REAL300000037641 none O=C([O-])C1=CC=CC(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
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, 1, 1, 1, 1, 1, 10, 10, 47, 107, 184, 184, 107, 184, 184, 184, 184, 1, 1, 1, 1, 10, 47, 107, 107, 184, 184, 184, 1] 184
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: 767
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037641 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037641
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037641/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037641
Building REAL300000037642
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037642'
/scratch/stefan/7769618/working/building/REAL300000037642 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037642

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037642/0 /scratch/stefan/7769618/working/building/REAL300000037642 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/716
`/scratch/stefan/7769618/working/3D/716' -> `0.mol2'
Preparing input files

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

`REAL300000037642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037642 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 13, 28, 34, 34, 28, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 7, 15, 15, 22, 32, 32, 1, 7, 7, 7, 13, 28, 28, 34, 34, 34, 1, 1, 1, 15, 15, 15, 15, 22, 22, 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: 259
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: REAL300000037642 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 34, 34, 34, 34, 108, 134, 134, 201, 201, 201, 34, 13, 13, 13, 11, 3, 3, 1, 1, 1, 34, 34, 34, 134, 134, 134, 134, 201, 201, 34] 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: 694
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037642 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037642
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037642/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037642
Building REAL300000037643
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037643'
/scratch/stefan/7769618/working/building/REAL300000037643 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037643

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037643/0 /scratch/stefan/7769618/working/building/REAL300000037643 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/717
`/scratch/stefan/7769618/working/3D/717' -> `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=C(Cl)C=C1Cl)

`REAL300000037643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037643 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 65, 75, 75, 75, 75, 75, 75, 176, 201, 201, 201, 75, 75, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 75, 75, 75, 75, 75, 75, 201, 201, 75, 75, 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: 578
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037643 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 36, 75, 75, 75, 75, 75, 75, 75, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 12, 12, 1, 1, 36, 36, 75, 75, 75] 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: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037643 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037643
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037643/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037643
Building REAL300000037644
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037644'
/scratch/stefan/7769618/working/building/REAL300000037644 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037644

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037644/0 /scratch/stefan/7769618/working/building/REAL300000037644 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/718
`/scratch/stefan/7769618/working/3D/718' -> `0.mol2'
Preparing input files

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

`REAL300000037644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037644 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 79, 79, 53, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 11, 22, 22, 28, 28, 1, 8, 8, 8, 13, 53, 53, 79, 79, 79, 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: 422
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037644 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 79, 79, 79, 79, 79, 169, 201, 201, 201, 201, 79, 34, 34, 34, 21, 6, 6, 1, 1, 1, 79, 79, 79, 201, 201, 201, 201, 79] 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/7769618/working/building/REAL300000037644 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037644
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037644/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037644
Building REAL300000037645
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037645'
/scratch/stefan/7769618/working/building/REAL300000037645 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037645

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037645/0 /scratch/stefan/7769618/working/building/REAL300000037645 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/719
`/scratch/stefan/7769618/working/3D/719' -> `0.mol2'
Preparing input files

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

`REAL300000037645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037645 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 49, 117, 201, 201, 117, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 49, 117, 117, 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: 863
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037645 none CC(=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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: [103, 103, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 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: 337
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037645 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037645
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037645/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037645
Building REAL300000037646
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037646'
/scratch/stefan/7769618/working/building/REAL300000037646 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037646

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037646/0 /scratch/stefan/7769618/working/building/REAL300000037646 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/720
`/scratch/stefan/7769618/working/3D/720' -> `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=C(Cl)C=C2Cl)C1)

`REAL300000037646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037646 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 21, 88, 201, 201, 88, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 5, 5, 21, 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: 859
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037646 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 131, 201, 131, 131, 201, 201, 131, 201, 201, 131, 131, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 131, 201, 201, 131, 131, 37, 7, 7, 1, 1, 1, 131, 131] 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: 848
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037646 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 10, 52, 131, 131, 52, 131, 131, 131, 131, 1, 5, 5, 1, 5, 5, 1, 1, 10, 52, 52, 131, 131, 131, 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: 568
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037646 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037646
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037646/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037646
Building REAL300000037647
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037647'
/scratch/stefan/7769618/working/building/REAL300000037647 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037647

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037647/0 /scratch/stefan/7769618/working/building/REAL300000037647 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/721
`/scratch/stefan/7769618/working/3D/721' -> `0.mol2'
Preparing input files

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

`REAL300000037647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037647 none CC(N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 55, 127, 127, 55, 115, 127, 127, 127, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 55, 55, 127, 127, 127, 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: 530
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037647 none CC(N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [122, 54, 53, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 127, 127, 127, 127, 127, 201, 201, 201, 127, 127, 127, 122, 122, 122, 122, 8, 8, 1, 1, 1, 127, 127, 201, 201, 127, 127, 127, 127, 127, 127] 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: 850
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037647 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037647
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037647/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037647
Building REAL300000037648
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037648'
/scratch/stefan/7769618/working/building/REAL300000037648 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037648

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037648/0 /scratch/stefan/7769618/working/building/REAL300000037648 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/722
`/scratch/stefan/7769618/working/3D/722' -> `0.mol2'
Preparing input files

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

`REAL300000037648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037648 none CC(CCCCCCC(=O)[O-])N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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: [82, 35, 82, 110, 110, 114, 125, 128, 201, 201, 201, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 110, 110, 110, 110, 114, 114, 125, 125, 128, 128, 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: 892
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037648 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037648
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037648/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037648
Building REAL300000037649
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037649'
/scratch/stefan/7769618/working/building/REAL300000037649 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037649

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037649/0 /scratch/stefan/7769618/working/building/REAL300000037649 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/723
`/scratch/stefan/7769618/working/3D/723' -> `0.mol2'
Preparing input files

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

`REAL300000037649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037649 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 144, 201, 201, 201, 144, 144, 55, 54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 201, 201, 144, 144, 144, 144, 144, 8, 8, 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: 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: REAL300000037649 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 14, 14, 1, 1, 1, 1, 8, 8, 59, 144, 144, 59, 144, 144, 144, 144, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 59, 59, 144, 144, 144] 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: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037649 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037649
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037649/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037649
Building REAL300000037650
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037650'
/scratch/stefan/7769618/working/building/REAL300000037650 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037650

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037650/0 /scratch/stefan/7769618/working/building/REAL300000037650 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/724
`/scratch/stefan/7769618/working/3D/724' -> `0.mol2'
Preparing input files

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

`REAL300000037650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037650 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [183, 183, 183, 183, 183, 125, 125, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 183, 183, 183, 125, 37, 8, 8, 1, 1, 1, 183, 183] 183
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: 325
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037650 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 8, 47, 108, 183, 183, 108, 175, 183, 183, 183, 1, 1, 1, 8, 47, 108, 108, 183, 183, 183, 1, 1] 183
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: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037650 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037650
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037650/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037650
Building REAL300000037651
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037651'
/scratch/stefan/7769618/working/building/REAL300000037651 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037651

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037651/0 /scratch/stefan/7769618/working/building/REAL300000037651 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/725
`/scratch/stefan/7769618/working/3D/725' -> `0.mol2'
Preparing input files

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

`REAL300000037651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037651 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 44, 128, 176, 201, 201, 201, 201, 201, 201, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 176, 176, 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: 788
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037651 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 1, 1, 1, 3, 3, 1, 1, 1, 8, 28, 28, 110, 201, 201, 110, 201, 201, 201, 201, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 110, 110, 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: 858
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037651 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037651
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037651/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037651
Building REAL300000037652
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037652'
/scratch/stefan/7769618/working/building/REAL300000037652 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037652

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037652/0 /scratch/stefan/7769618/working/building/REAL300000037652 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/726
`/scratch/stefan/7769618/working/3D/726' -> `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=C(Cl)C=C1Cl)

`REAL300000037652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037652 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
201  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, 129, 129, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 129, 37, 8, 8, 1, 1, 1] 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])
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: REAL300000037652 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
201  conformations 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, 12, 12, 51, 135, 201, 201, 135, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 12, 51, 135, 135, 201, 201, 201] 201
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: 869
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037652 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037652
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037652/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037652
Building REAL300000037653
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037653'
/scratch/stefan/7769618/working/building/REAL300000037653 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037653

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037653/0 /scratch/stefan/7769618/working/building/REAL300000037653 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/727
`/scratch/stefan/7769618/working/3D/727' -> `0.mol2'
Preparing input files

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

`REAL300000037653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037653 none O=C([O-])C1=CC=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 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, 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, 147, 147, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 41, 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: REAL300000037653 none O=C([O-])C1=CC=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 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, 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, 116, 201, 201, 116, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 46, 116, 116, 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: 832
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037653 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037653
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037653/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037653
Building REAL300000037654
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037654'
/scratch/stefan/7769618/working/building/REAL300000037654 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037654

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037654/0 /scratch/stefan/7769618/working/building/REAL300000037654 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/728
`/scratch/stefan/7769618/working/3D/728' -> `0.mol2'
Preparing input files

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

`REAL300000037654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037654 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 111, 111, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 111, 33, 6, 6, 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: 366
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037654 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 7, 7, 36, 92, 201, 201, 92, 197, 201, 201, 201, 1, 1, 1, 1, 1, 7, 36, 92, 92, 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: 857
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037654 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037654
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037654/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037654
Building REAL300000037655
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037655'
/scratch/stefan/7769618/working/building/REAL300000037655 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037655

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037655/0 /scratch/stefan/7769618/working/building/REAL300000037655 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/729
`/scratch/stefan/7769618/working/3D/729' -> `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=C(Cl)C=C2Cl)O1)

`REAL300000037655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037655 none O=C([O-])C=CC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 136, 136, 136, 136, 108, 108, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 136, 136, 108, 35, 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: 463
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037655 none O=C([O-])C=CC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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: [21, 10, 22, 10, 1, 1, 1, 1, 1, 1, 4, 4, 18, 72, 136, 136, 72, 134, 136, 136, 136, 1, 10, 10, 1, 1, 4, 18, 72, 72, 136, 136, 136] 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: 636
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037655 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037655
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037655/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037655
Building REAL300000037656
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037656'
/scratch/stefan/7769618/working/building/REAL300000037656 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037656

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037656/0 /scratch/stefan/7769618/working/building/REAL300000037656 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/730
`/scratch/stefan/7769618/working/3D/730' -> `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=C(Cl)C=C3Cl)C2=C1)

`REAL300000037656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037656 none O=C([O-])C1=CC=C2NC=C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 149, 149, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 149, 39, 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: 335
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: REAL300000037656 none O=C([O-])C1=CC=C2NC=C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 45, 109, 201, 201, 109, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 44, 109, 109, 201, 201, 201, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 35, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 814
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037656 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037656
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037656/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037656
Building REAL300000037657
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037657'
/scratch/stefan/7769618/working/building/REAL300000037657 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037657

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037657/0 /scratch/stefan/7769618/working/building/REAL300000037657 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/731
`/scratch/stefan/7769618/working/3D/731' -> `0.mol2'
Preparing input files

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

`REAL300000037657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037657 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 111, 38, 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: 376
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037657 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 11, 11, 55, 107, 201, 201, 107, 201, 201, 201, 201, 1, 1, 1, 1, 11, 55, 107, 107, 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: 821
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037657 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037657
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037657/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037657
Building REAL300000037658
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037658'
/scratch/stefan/7769618/working/building/REAL300000037658 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037658

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037658/0 /scratch/stefan/7769618/working/building/REAL300000037658 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/732
`/scratch/stefan/7769618/working/3D/732' -> `0.mol2'
Preparing input files

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

`REAL300000037658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037658 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 112, 112, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 112, 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: 773
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037658 none O=C([O-])C1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 9, 9, 39, 96, 201, 201, 96, 192, 201, 201, 201, 1, 1, 1, 1, 1, 9, 39, 96, 96, 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: 843
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037658 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037658
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037658/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037658
Building REAL300000037659
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037659'
/scratch/stefan/7769618/working/building/REAL300000037659 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037659

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037659/0 /scratch/stefan/7769618/working/building/REAL300000037659 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/733
`/scratch/stefan/7769618/working/3D/733' -> `0.mol2'
Preparing input files

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

`REAL300000037659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037659 none CC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
201  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, 113, 113, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 37, 8, 8, 1, 1, 1, 201] 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])
total number of confs: 345
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037659 none CC1=CC=C(C=NNCC2=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
201  conformations 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, 8, 8, 42, 112, 201, 201, 111, 201, 201, 201, 201, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 41, 112, 112, 201, 201, 201, 1] 201
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: 860
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037659 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037659
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037659/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037659
Building REAL300000037660
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037660'
/scratch/stefan/7769618/working/building/REAL300000037660 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037660

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037660/0 /scratch/stefan/7769618/working/building/REAL300000037660 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/734
`/scratch/stefan/7769618/working/3D/734' -> `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=C(Cl)C=C2Cl)=C1)

`REAL300000037660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037660 none O=C([O-])C1=C(Cl)SC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 100, 100, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 100, 33, 6, 6, 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: 350
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037660 none O=C([O-])C1=C(Cl)SC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 9, 9, 38, 108, 201, 201, 108, 201, 201, 201, 201, 1, 9, 38, 108, 108, 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: 860
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037660 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037660
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037660/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037660
Building REAL300000037661
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037661'
/scratch/stefan/7769618/working/building/REAL300000037661 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037661

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037661/0 /scratch/stefan/7769618/working/building/REAL300000037661 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/735
`/scratch/stefan/7769618/working/3D/735' -> `0.mol2'
Preparing input files

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

`REAL300000037661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037661 none CN1N=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [178, 178, 178, 178, 178, 178, 178, 178, 127, 127, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 127, 42, 8, 8, 1, 1, 1] 178
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: 324
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037661 none CN1N=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 120, 178, 178, 178, 178, 178, 178, 178, 2, 2, 2, 1, 10, 49, 120, 120, 178, 178, 178] 178
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: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037661 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037661
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037661/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037661
Building REAL300000037662
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037662'
/scratch/stefan/7769618/working/building/REAL300000037662 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037662

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037662/0 /scratch/stefan/7769618/working/building/REAL300000037662 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/736
`/scratch/stefan/7769618/working/3D/736' -> `0.mol2'
Preparing input files

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

`REAL300000037662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037662 none CN1C=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 177, 177, 177, 177, 177, 177, 128, 128, 43, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 128, 43, 8, 8, 1, 1, 1] 177
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: 321
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037662 none CN1C=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 47, 116, 177, 177, 116, 177, 177, 177, 177, 2, 2, 2, 1, 1, 8, 47, 116, 116, 177, 177, 177] 177
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: 734
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037662 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037662
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037662/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037662
Building REAL300000037663
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037663'
/scratch/stefan/7769618/working/building/REAL300000037663 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037663

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037663/0 /scratch/stefan/7769618/working/building/REAL300000037663 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/737
`/scratch/stefan/7769618/working/3D/737' -> `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=C(Cl)C=C1Cl)

`REAL300000037663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037663 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 125, 125, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 165, 125, 37, 8, 8, 1, 1, 1] 165
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: 284
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: REAL300000037663 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 30, 75, 165, 165, 75, 165, 165, 165, 165, 4, 4, 4, 4, 4, 4, 1, 1, 1, 6, 30, 75, 75, 165, 165, 165] 165
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 30, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 695
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037663 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037663
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037663/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037663
Building REAL300000037664
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037664'
/scratch/stefan/7769618/working/building/REAL300000037664 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037664

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037664/0 /scratch/stefan/7769618/working/building/REAL300000037664 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/738
`/scratch/stefan/7769618/working/3D/738' -> `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=C(Cl)C=C1Cl)

`REAL300000037664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037664 none COC1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 125, 125, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 125, 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: 341
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037664 none COC1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 2, 2, 1, 1, 1, 6, 6, 39, 114, 201, 201, 114, 183, 201, 201, 201, 4, 4, 4, 1, 1, 1, 6, 39, 114, 114, 201, 201, 201] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27, 28] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037664 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037664
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037664/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037664
Building REAL300000037665
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037665'
/scratch/stefan/7769618/working/building/REAL300000037665 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037665

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037665/0 /scratch/stefan/7769618/working/building/REAL300000037665 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/739
`/scratch/stefan/7769618/working/3D/739' -> `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=C(Cl)C=C3Cl)C2=C1)

`REAL300000037665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037665 none O=C([O-])C1=CC=C2SC=C(C=NNCC3=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [199, 199, 199, 199, 199, 199, 199, 199, 199, 143, 143, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 143, 39, 8, 8, 1, 1, 1, 199] 199
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: REAL300000037665 none O=C([O-])C1=CC=C2SC=C(C=NNCC3=CC=C(Cl)C=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', '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, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 39, 109, 199, 199, 109, 199, 199, 199, 199, 1, 1, 1, 1, 1, 10, 38, 109, 109, 199, 199, 199, 1] 199
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: 800
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037665 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037665
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037665/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037665
Building REAL300000037666
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037666'
/scratch/stefan/7769618/working/building/REAL300000037666 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037666

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037666/0 /scratch/stefan/7769618/working/building/REAL300000037666 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/740
`/scratch/stefan/7769618/working/3D/740' -> `0.mol2'
Preparing input files

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

`REAL300000037666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037666 none O=C([O-])C1=COC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 129, 129, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 189, 189, 129, 37, 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: 333
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037666 none O=C([O-])C1=COC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 7, 7, 45, 110, 189, 189, 110, 189, 189, 189, 189, 1, 1, 7, 45, 110, 110, 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: 785
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037666 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037666
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037666/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037666
Building REAL300000037667
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037667'
/scratch/stefan/7769618/working/building/REAL300000037667 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037667

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037667/0 /scratch/stefan/7769618/working/building/REAL300000037667 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/741
`/scratch/stefan/7769618/working/3D/741' -> `0.mol2'
Preparing input files

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

`REAL300000037667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037667 none COC1=CC(C=NNCC2=CC=C(Cl)C=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', '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, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 163, 163, 163, 72, 72, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 201, 201, 201, 201, 201, 163, 72, 34, 6, 6, 1, 1, 1, 163, 163] 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: 520
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037667 none COC1=CC(C=NNCC2=CC=C(Cl)C=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', '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, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 9, 9, 27, 102, 163, 163, 102, 158, 163, 163, 163, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 27, 102, 102, 163, 163, 163, 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: 652
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037667 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037667
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037667/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037667
Building REAL300000037668
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037668'
/scratch/stefan/7769618/working/building/REAL300000037668 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037668

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037668/0 /scratch/stefan/7769618/working/building/REAL300000037668 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/742
`/scratch/stefan/7769618/working/3D/742' -> `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=C(Cl)C=C2Cl)C(F)=C1)

`REAL300000037668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037668 none O=C([O-])C1=CC(F)=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
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, 124, 137, 137, 137, 122, 122, 43, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 122, 43, 8, 8, 1, 1, 1, 137] 137
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: 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: REAL300000037668 none O=C([O-])C1=CC(F)=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 56, 91, 137, 137, 137, 137, 137, 137, 137, 1, 1, 1, 1, 7, 56, 91, 91, 137, 137, 137, 1] 137
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: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037668 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037668
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037668/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037668
Building REAL300000037669
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037669'
/scratch/stefan/7769618/working/building/REAL300000037669 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037669

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037669/0 /scratch/stefan/7769618/working/building/REAL300000037669 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/743
`/scratch/stefan/7769618/working/3D/743' -> `0.mol2'
Preparing input files

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

`REAL300000037669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037669 none CC1=C(C(=O)[O-])NC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
201  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, 144, 144, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 144, 39, 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: 343
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037669 none CC1=C(C(=O)[O-])NC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
201  conformations 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, 106, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 8, 31, 106, 106, 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: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037669 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037669
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037669/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037669
Building REAL300000037670
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037670'
/scratch/stefan/7769618/working/building/REAL300000037670 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037670

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037670/0 /scratch/stefan/7769618/working/building/REAL300000037670 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/744
`/scratch/stefan/7769618/working/3D/744' -> `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=C(Cl)C=C2Cl)=C1O)

`REAL300000037670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037670 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 106, 106, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 106, 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: 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: REAL300000037670 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 11, 11, 36, 115, 201, 201, 115, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 11, 36, 115, 115, 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: 853
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037670 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037670
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037670/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037670
Building REAL300000037671
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037671'
/scratch/stefan/7769618/working/building/REAL300000037671 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037671

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037671/0 /scratch/stefan/7769618/working/building/REAL300000037671 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/745
`/scratch/stefan/7769618/working/3D/745' -> `0.mol2'
Preparing input files

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

`REAL300000037671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037671 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [179, 179, 179, 179, 179, 131, 131, 43, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 131, 43, 8, 8, 1, 1, 1, 179] 179
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: 325
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037671 none O=C([O-])C1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 9, 48, 97, 179, 179, 179, 179, 179, 179, 179, 1, 1, 1, 9, 48, 97, 97, 179, 179, 179, 1] 179
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: 443
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037671 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037671
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037671/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037671
Building REAL300000037672
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037672'
/scratch/stefan/7769618/working/building/REAL300000037672 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037672

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037672/0 /scratch/stefan/7769618/working/building/REAL300000037672 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/746
`/scratch/stefan/7769618/working/3D/746' -> `0.mol2'
Preparing input files

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

`REAL300000037672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037672 none CCOC1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 136, 201, 201, 201, 79, 79, 79, 79, 79, 42, 19, 12, 4, 4, 1, 1, 1, 42, 42, 201, 201] 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: 681
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037672 none CCOC1=CC(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 35, 42, 42, 35, 42, 42, 42, 42, 1, 1, 1, 1, 7, 20, 32, 32, 5, 5, 5, 5, 5, 1, 7, 11, 35, 35, 42, 42, 42, 1, 1, 20, 20] 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: 297
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037672 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037672
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037672/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037672
Building REAL300000037673
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037673'
/scratch/stefan/7769618/working/building/REAL300000037673 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037673

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037673/0 /scratch/stefan/7769618/working/building/REAL300000037673 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/747
`/scratch/stefan/7769618/working/3D/747' -> `0.mol2'
Preparing input files

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

`REAL300000037673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037673 none O=C([O-])CCC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 190, 187, 96, 96, 96, 96, 71, 71, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 187, 187, 96, 96, 71, 33, 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: 728
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037673 none O=C([O-])CCC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [23, 13, 15, 9, 1, 1, 1, 1, 1, 1, 4, 4, 12, 51, 96, 96, 96, 96, 96, 96, 96, 1, 13, 13, 9, 9, 1, 1, 4, 12, 51, 51, 96, 96, 96] 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: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037673 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037673
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037673/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037673
Building REAL300000037674
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037674'
/scratch/stefan/7769618/working/building/REAL300000037674 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037674

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037674/0 /scratch/stefan/7769618/working/building/REAL300000037674 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/748
`/scratch/stefan/7769618/working/3D/748' -> `0.mol2'
Preparing input files

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

`REAL300000037674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037674 none O=C([O-])C1=C2NC=C(C=NNCC3=CC=C(Cl)C=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', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 124, 124, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 124, 36, 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: 355
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037674 none O=C([O-])C1=C2NC=C(C=NNCC3=CC=C(Cl)C=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', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 12, 12, 49, 112, 201, 201, 112, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 12, 49, 113, 113, 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: 838
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037674 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037674
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037674/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037674
Building REAL300000037675
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037675'
/scratch/stefan/7769618/working/building/REAL300000037675 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037675

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037675/0 /scratch/stefan/7769618/working/building/REAL300000037675 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/749
`/scratch/stefan/7769618/working/3D/749' -> `0.mol2'
Preparing input files

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

`REAL300000037675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037675 none O=C([O-])C1=CC2=CC(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 111, 111, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 111, 37, 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: 371
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037675 none O=C([O-])C1=CC2=CC(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 11, 11, 44, 98, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 11, 44, 98, 98, 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: 486
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037675 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037675
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037675/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037675
Building REAL300000037676
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037676'
/scratch/stefan/7769618/working/building/REAL300000037676 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037676

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037676/0 /scratch/stefan/7769618/working/building/REAL300000037676 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/750
`/scratch/stefan/7769618/working/3D/750' -> `0.mol2'
Preparing input files

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

`REAL300000037676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037676 none O=C([O-])C1=CN=C2C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [195, 195, 195, 195, 195, 195, 195, 131, 131, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 195, 131, 41, 8, 8, 1, 1, 1, 195, 195, 195] 195
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: 347
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: REAL300000037676 none O=C([O-])C1=CN=C2C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 120, 195, 195, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 9, 50, 120, 120, 195, 195, 195, 1, 1, 1] 195
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: 530
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037676 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037676
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037676/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037676
Building REAL300000037677
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037677'
/scratch/stefan/7769618/working/building/REAL300000037677 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037677

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037677/0 /scratch/stefan/7769618/working/building/REAL300000037677 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/751
`/scratch/stefan/7769618/working/3D/751' -> `0.mol2'
Preparing input files

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

`REAL300000037677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037677 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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, 167, 84, 61, 84, 84, 37, 37, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 201, 201, 84, 84, 37, 19, 5, 5, 1, 1, 1, 84] 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: 561
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037677 none O=C([O-])COC1=CC=C(C=NNCC2=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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: [37, 23, 37, 7, 1, 1, 1, 1, 1, 1, 6, 6, 14, 63, 84, 84, 63, 83, 84, 84, 84, 1, 1, 1, 23, 23, 1, 1, 6, 14, 63, 63, 84, 84, 84, 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: 469
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037677 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037677
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037677/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037677
Building REAL300000037678
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037678'
/scratch/stefan/7769618/working/building/REAL300000037678 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037678

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037678/0 /scratch/stefan/7769618/working/building/REAL300000037678 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/752
`/scratch/stefan/7769618/working/3D/752' -> `0.mol2'
Preparing input files

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

`REAL300000037678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037678 none O=C([O-])C1=CC2=C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 98, 98, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 98, 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: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037678 none O=C([O-])C1=CC2=C(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 12, 12, 47, 125, 201, 201, 125, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 12, 47, 125, 125, 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: 818
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037678 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037678
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037678/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037678
Building REAL300000037679
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037679'
/scratch/stefan/7769618/working/building/REAL300000037679 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037679

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037679/0 /scratch/stefan/7769618/working/building/REAL300000037679 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/753
`/scratch/stefan/7769618/working/3D/753' -> `0.mol2'
Preparing input files

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

`REAL300000037679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037679 none COC1=CC(C(=O)[O-])=CC=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 143, 143, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 143, 41, 8, 8, 1, 1, 1] 177
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: 302
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: REAL300000037679 none COC1=CC(C(=O)[O-])=CC=C1C=NNCC1=CC=C(Cl)C=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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 100, 177, 177, 100, 146, 177, 177, 177, 3, 3, 3, 1, 1, 1, 7, 31, 100, 100, 177, 177, 177] 177
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: 710
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037679 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037679
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037679/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037679
Building REAL300000037680
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037680'
/scratch/stefan/7769618/working/building/REAL300000037680 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037680

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037680/0 /scratch/stefan/7769618/working/building/REAL300000037680 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/754
`/scratch/stefan/7769618/working/3D/754' -> `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=C(Cl)C=C3Cl)=N2)C1)

`REAL300000037680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037680 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 12, 21, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 12, 49, 88, 88, 49, 86, 88, 88, 88, 1, 12, 12, 12, 1, 1, 4, 12, 49, 49, 88, 88, 88, 12, 12] 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: 413
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037680 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 88, 201, 88, 88, 88, 70, 70, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 88, 88, 70, 32, 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: 494
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037680 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=C(Cl)C=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', 'Cl', 'C.ar', '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, 16, 1, 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, 12, 12, 12, 12, 20, 20, 42, 123, 201, 201, 123, 201, 201, 201, 201, 12, 1, 1, 1, 12, 12, 20, 42, 123, 123, 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: 841
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037680 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037680
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037680/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037680
Building REAL300000037681
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037681'
/scratch/stefan/7769618/working/building/REAL300000037681 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037681

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037681/0 /scratch/stefan/7769618/working/building/REAL300000037681 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/755
`/scratch/stefan/7769618/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1)

`REAL300000037681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037681 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 86, 151, 151, 86, 86, 86, 37, 37, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 86, 86, 151, 151, 86, 86, 4, 4, 1, 1, 1, 1, 86] 151
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 526
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037681 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 32, 86, 86, 32, 86, 87, 87, 86, 86, 1, 1, 5, 5, 1, 1, 32, 32, 86, 86, 86, 86, 1] 151
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037681 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037681/1 /scratch/stefan/7769618/working/building/REAL300000037681 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/756
`/scratch/stefan/7769618/working/3D/756' -> `1.mol2'
Preparing input files

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

`REAL300000037681.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037681/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037681 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 14, 29, 29, 14, 14, 14, 12, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 29, 29, 14, 14, 12, 6, 1, 1, 1, 1, 14] 29
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037681 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 5, 5, 1, 1, 4, 14, 14, 14, 14, 14, 1] 29
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037681 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037681
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037681/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037681/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037681
Building REAL300000037682
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037682'
/scratch/stefan/7769618/working/building/REAL300000037682 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037682

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037682/0 /scratch/stefan/7769618/working/building/REAL300000037682 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/757
`/scratch/stefan/7769618/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1)

`REAL300000037682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037682 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 78, 78, 44, 44, 44, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 45, 45, 44, 44, 78, 78, 44, 44, 6, 6, 1, 1, 1, 1, 27, 27, 44] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 397
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037682 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 4, 4, 20, 44, 44, 25, 44, 44, 44, 91, 163, 163, 163, 1, 1, 4, 4, 1, 1, 20, 20, 44, 44, 44, 44, 163, 163, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037682 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037682
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037682/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037682
Building REAL300000037683
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037683'
/scratch/stefan/7769618/working/building/REAL300000037683 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037683

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037683/0 /scratch/stefan/7769618/working/building/REAL300000037683 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/758
`/scratch/stefan/7769618/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=CC=C1OCC(=O)[O-])

`REAL300000037683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037683 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [79, 45, 45, 45, 12, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 45, 45, 45, 45, 101, 166, 170, 170, 79, 79, 79, 45, 12, 12, 1, 1, 4, 4, 1, 45, 45, 166, 166] 201
rigid atoms, others: [32, 33, 36, 7, 8, 9, 10, 11, 12, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40])
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: REAL300000037683 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [3, 1, 1, 1, 1, 1, 6, 40, 40, 45, 45, 45, 45, 64, 64, 64, 45, 45, 1, 1, 1, 1, 7, 13, 17, 17, 3, 3, 3, 1, 6, 6, 45, 45, 64, 64, 45, 1, 1, 13, 13] 201
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: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037683 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037683/1 /scratch/stefan/7769618/working/building/REAL300000037683 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/759
`/scratch/stefan/7769618/working/3D/759' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=CC=C1OCC(=O)[O-])

`REAL300000037683.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037683/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037683 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [25, 15, 15, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 15, 15, 15, 15, 52, 87, 87, 87, 25, 25, 25, 15, 4, 2, 1, 1, 5, 5, 1, 15, 15, 87, 87] 201
rigid atoms, others: [32, 33, 36, 7, 8, 9, 10, 11, 12, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40])
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: REAL300000037683 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [3, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 43, 43, 43, 15, 15, 1, 1, 1, 1, 9, 28, 35, 35, 3, 3, 3, 1, 7, 15, 15, 15, 43, 43, 15, 1, 1, 28, 28] 201
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: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037683 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037683
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037683/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037683/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037683
Building REAL300000037684
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037684'
/scratch/stefan/7769618/working/building/REAL300000037684 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037684

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037684/0 /scratch/stefan/7769618/working/building/REAL300000037684 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/760
`/scratch/stefan/7769618/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1)

`REAL300000037684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037684 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 64, 64, 40, 40, 40, 23, 23, 3, 1, 1, 1, 1, 1, 1, 6, 16, 30, 30, 1, 1, 40, 40, 64, 64, 40, 40, 3, 3, 1, 1, 16, 16, 1, 1, 40] 201
rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36])
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: REAL300000037684 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 4, 4, 18, 40, 40, 18, 39, 128, 176, 180, 180, 40, 40, 1, 1, 4, 4, 1, 1, 18, 18, 40, 40, 176, 176, 40, 40, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037684 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037684/1 /scratch/stefan/7769618/working/building/REAL300000037684 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/761
`/scratch/stefan/7769618/working/3D/761' -> `1.mol2'
Preparing input files

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

`REAL300000037684.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037684/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037684 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 50, 50, 20, 20, 20, 14, 4, 4, 1, 1, 1, 1, 1, 1, 5, 23, 34, 34, 1, 1, 20, 20, 50, 50, 20, 20, 14, 4, 1, 1, 23, 23, 1, 1, 20] 201
rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36])
total number of confs: 292
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: REAL300000037684 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 14, 14, 20, 20, 14, 14, 42, 76, 76, 76, 20, 20, 1, 1, 5, 5, 1, 1, 4, 14, 20, 20, 76, 76, 20, 20, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 259
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037684 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037684
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037684/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037684/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037684
Building REAL300000037685
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037685'
/scratch/stefan/7769618/working/building/REAL300000037685 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037685

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037685/0 /scratch/stefan/7769618/working/building/REAL300000037685 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/762
`/scratch/stefan/7769618/working/3D/762' -> `0.mol2'
Preparing input files

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

`REAL300000037685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037685 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens 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, 24, 24, 34, 34, 34, 34, 64, 64, 64, 34, 34, 1, 1, 1, 1, 1, 1, 6, 19, 31, 31, 1, 6, 6, 6, 6, 34, 34, 64, 64, 34, 1, 1, 1, 19, 19, 1] 201
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: 309
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: REAL300000037685 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens 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, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 14, 34, 34, 34, 34, 34, 103, 159, 160, 160, 34, 14, 14, 14, 14, 1, 1, 4, 4, 1, 34, 34, 34, 159, 159, 34] 201
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 29, 30] set([0, 1, 2, 9, 10, 11, 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: 477
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037685 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037685/1 /scratch/stefan/7769618/working/building/REAL300000037685 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/763
`/scratch/stefan/7769618/working/3D/763' -> `1.mol2'
Preparing input files

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

`REAL300000037685.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037685/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037685 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens 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, 20, 20, 20, 20, 20, 51, 51, 51, 20, 20, 1, 1, 1, 1, 1, 1, 5, 13, 17, 17, 1, 9, 9, 9, 20, 20, 20, 51, 51, 20, 1, 1, 1, 13, 13, 1] 201
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: 245
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037685 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens 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, 4, 4, 4, 1, 1, 6, 20, 20, 20, 20, 20, 50, 78, 78, 78, 20, 6, 6, 6, 2, 1, 1, 5, 5, 1, 20, 20, 20, 78, 78, 20] 201
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 29, 30] set([0, 1, 2, 9, 10, 11, 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: 230
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037685 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037685
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037685/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037685/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037685
Building REAL300000037686
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037686'
/scratch/stefan/7769618/working/building/REAL300000037686 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037686

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037686/0 /scratch/stefan/7769618/working/building/REAL300000037686 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/764
`/scratch/stefan/7769618/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037686 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 25, 55, 55, 25, 25, 25, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 25, 55, 55, 25, 25, 22, 6, 1, 1, 1, 1, 25] 55
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037686 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 5, 5, 1, 1, 5, 15, 25, 25, 25, 25, 1] 55
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037686 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037686/1 /scratch/stefan/7769618/working/building/REAL300000037686 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/765
`/scratch/stefan/7769618/working/3D/765' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037686.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037686/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037686 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 79, 201, 201, 79, 79, 79, 46, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 79, 79, 201, 201, 79, 79, 8, 8, 1, 1, 1, 1, 79] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
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: REAL300000037686 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 27, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 5, 5, 1, 1, 27, 27, 79, 79, 79, 79, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 172
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037686 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037686
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037686/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037686/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037686
Building REAL300000037687
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037687'
/scratch/stefan/7769618/working/building/REAL300000037687 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037687

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037687/0 /scratch/stefan/7769618/working/building/REAL300000037687 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/766
`/scratch/stefan/7769618/working/3D/766' -> `0.mol2'
Preparing input files

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

`REAL300000037687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037687 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 43, 43, 59, 59, 59, 59, 109, 109, 109, 59, 59, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 59, 59, 109, 109, 59, 1, 1, 1, 1] 109
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 345
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037687 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [37, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 37, 59, 59, 37, 56, 59, 59, 59, 59, 37, 37, 37, 37, 1, 1, 5, 5, 1, 59, 59, 59, 59] 109
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 270
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037687 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037687/1 /scratch/stefan/7769618/working/building/REAL300000037687 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/767
`/scratch/stefan/7769618/working/3D/767' -> `1.mol2'
Preparing input files

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

`REAL300000037687.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037687/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037687 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 23, 25, 25, 25, 25, 50, 50, 50, 25, 25, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 23, 25, 25, 50, 50, 25, 1, 1, 1, 1] 50
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 179
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037687 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 14, 25, 25, 14, 18, 25, 25, 25, 25, 14, 14, 14, 4, 1, 1, 5, 5, 1, 25, 25, 25, 25] 50
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 105
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037687 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037687
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037687/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037687/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037687
Building REAL300000037688
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037688'
/scratch/stefan/7769618/working/building/REAL300000037688 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037688

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037688/0 /scratch/stefan/7769618/working/building/REAL300000037688 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/768
`/scratch/stefan/7769618/working/3D/768' -> `0.mol2'
Preparing input files

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

`REAL300000037688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037688 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [7, 1, 7, 39, 39, 76, 76, 76, 76, 173, 173, 173, 76, 76, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 7, 76, 76, 173, 173, 76, 1, 1, 2, 2, 1, 1] 201
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: 597
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037688 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [34, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 34, 76, 76, 34, 34, 102, 111, 111, 76, 76, 34, 34, 34, 34, 1, 1, 5, 5, 1, 76, 76, 102, 102, 76, 76] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 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: 579
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037688 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037688/1 /scratch/stefan/7769618/working/building/REAL300000037688 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/769
`/scratch/stefan/7769618/working/3D/769' -> `1.mol2'
Preparing input files

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

`REAL300000037688.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037688/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037688 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(CC(=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 27, 37, 37, 37, 37, 88, 88, 88, 37, 37, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 27, 37, 37, 88, 88, 37, 1, 1, 2, 2, 1, 1] 137
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: 321
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037688 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(CC(=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 37, 37, 28, 34, 59, 65, 65, 37, 37, 20, 20, 20, 4, 1, 1, 5, 5, 1, 37, 37, 59, 59, 37, 37] 137
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 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: 268
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037688 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037688
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037688/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037688/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037688
Building REAL300000037689
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037689'
/scratch/stefan/7769618/working/building/REAL300000037689 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037689

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037689/0 /scratch/stefan/7769618/working/building/REAL300000037689 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/770
`/scratch/stefan/7769618/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=C(S(N)(=O)=O)C=N1)CCC2)

`REAL300000037689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037689 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 11, 11, 11, 11, 11, 11, 4, 1, 1, 5, 5, 1, 11, 11, 11, 11, 11, 11] 40
rigid atoms, others: [33, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 34
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: REAL300000037689 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 11, 40, 40, 40, 11, 11, 1, 1, 1, 2, 2, 2, 8, 11, 11, 40, 40, 11, 1, 1, 1, 1, 1, 1] 40
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: 150
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037689 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037689/1 /scratch/stefan/7769618/working/building/REAL300000037689 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/771
`/scratch/stefan/7769618/working/3D/771' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CC=C(S(N)(=O)=O)C=N1)CCC2)

`REAL300000037689.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037689/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037689 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [26, 26, 26, 26, 38, 38, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1, 5, 5, 1, 26, 26, 26, 26, 26, 26] 72
rigid atoms, others: [33, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037689 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 72, 72, 72, 26, 26, 1, 1, 1, 2, 2, 2, 1, 26, 26, 72, 72, 26, 1, 1, 1, 1, 1, 1] 72
rigid atoms, others: [0, 1, 2, 3, 36, 37, 6, 7, 8, 9, 10, 39, 34, 35, 22, 23, 24, 38, 28] set([32, 33, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037689 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037689
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037689/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037689/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037689
Building REAL300000037690
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037690'
/scratch/stefan/7769618/working/building/REAL300000037690 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037690

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037690/0 /scratch/stefan/7769618/working/building/REAL300000037690 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/772
`/scratch/stefan/7769618/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)N=C1)

`REAL300000037690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037690 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 77, 77, 40, 40, 40, 23, 23, 3, 1, 1, 1, 1, 1, 1, 6, 6, 7, 13, 13, 1, 1, 40, 40, 77, 77, 40, 40, 3, 3, 1, 1, 6, 6, 6, 6, 1, 1, 40] 201
rigid atoms, others: [32, 37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
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: REAL300000037690 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 2, 2, 16, 40, 40, 16, 39, 157, 157, 158, 167, 167, 40, 40, 1, 1, 4, 4, 1, 1, 16, 16, 40, 40, 157, 157, 157, 157, 40, 40, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037690 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037690/1 /scratch/stefan/7769618/working/building/REAL300000037690 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/773
`/scratch/stefan/7769618/working/3D/773' -> `1.mol2'
Preparing input files

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

`REAL300000037690.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037690/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037690 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 20, 46, 46, 20, 20, 20, 14, 4, 4, 1, 1, 1, 1, 1, 1, 6, 25, 33, 46, 38, 1, 1, 20, 20, 46, 46, 20, 20, 14, 4, 1, 1, 25, 25, 33, 33, 1, 1, 20] 201
rigid atoms, others: [32, 37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 319
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: REAL300000037690 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 14, 14, 20, 20, 14, 14, 48, 83, 91, 96, 94, 20, 20, 1, 1, 5, 5, 1, 1, 4, 14, 20, 20, 83, 83, 91, 91, 20, 20, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 339
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037690 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037690
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037690/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037690/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037690
Building REAL300000037691
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037691'
/scratch/stefan/7769618/working/building/REAL300000037691 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037691

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037691/0 /scratch/stefan/7769618/working/building/REAL300000037691 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/774
`/scratch/stefan/7769618/working/3D/774' -> `0.mol2'
Preparing input files

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

`REAL300000037691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037691 none CC(OC1=CC=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [168, 128, 44, 44, 44, 44, 44, 16, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 44, 168, 175, 175, 168, 168, 168, 168, 44, 44, 44, 16, 16, 1, 1, 4, 4, 1, 44] 201
rigid atoms, others: [34, 35, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 467
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037691 none CC(OC1=CC=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [15, 7, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 44, 44, 44, 44, 74, 74, 74, 44, 44, 1, 15, 20, 20, 15, 15, 15, 15, 1, 1, 1, 7, 7, 44, 44, 74, 74, 44, 1] 201
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: 298
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037691 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037691/1 /scratch/stefan/7769618/working/building/REAL300000037691 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/775
`/scratch/stefan/7769618/working/3D/775' -> `1.mol2'
Preparing input files

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

`REAL300000037691.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037691/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037691 none CC(OC1=CC=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [97, 62, 20, 20, 20, 20, 20, 8, 8, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 97, 97, 97, 97, 97, 97, 97, 20, 20, 20, 8, 3, 1, 1, 5, 5, 1, 20] 201
rigid atoms, others: [34, 35, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 295
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037691 none CC(OC1=CC=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [24, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 20, 20, 20, 20, 48, 48, 48, 20, 20, 1, 24, 29, 29, 24, 24, 24, 24, 1, 1, 1, 7, 19, 20, 20, 48, 48, 20, 1] 201
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: 268
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037691 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037691
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037691/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037691/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037691
Building REAL300000037692
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037692'
/scratch/stefan/7769618/working/building/REAL300000037692 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037692

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037692/0 /scratch/stefan/7769618/working/building/REAL300000037692 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/776
`/scratch/stefan/7769618/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)N=C1)

`REAL300000037692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037692 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 61, 61, 48, 48, 48, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 6, 11, 12, 17, 14, 1, 48, 48, 61, 61, 48, 48, 6, 6, 1, 1, 1, 11, 11, 11, 11, 1, 48] 201
rigid atoms, others: [32, 33, 38, 10, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 39])
total number of confs: 210
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037692 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 14, 48, 48, 48, 48, 48, 160, 165, 165, 175, 170, 48, 1, 1, 3, 3, 1, 1, 14, 14, 48, 48, 48, 165, 165, 165, 165, 48, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 319
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037692 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037692/1 /scratch/stefan/7769618/working/building/REAL300000037692 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/777
`/scratch/stefan/7769618/working/3D/777' -> `1.mol2'
Preparing input files

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

`REAL300000037692.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037692/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037692 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens 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, 22, 56, 56, 22, 22, 22, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 19, 24, 32, 30, 1, 22, 22, 56, 56, 22, 22, 19, 6, 1, 1, 1, 19, 19, 24, 24, 1, 22] 201
rigid atoms, others: [32, 33, 38, 10, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 39])
total number of confs: 310
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: REAL300000037692 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 9, 9, 22, 22, 22, 22, 22, 66, 90, 97, 117, 116, 22, 1, 1, 5, 5, 1, 1, 4, 9, 22, 22, 22, 90, 90, 97, 97, 22, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 350
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037692 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037692
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037692/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037692/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037692
Building REAL300000037693
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037693'
/scratch/stefan/7769618/working/building/REAL300000037693 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037693

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037693/0 /scratch/stefan/7769618/working/building/REAL300000037693 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/778
`/scratch/stefan/7769618/working/3D/778' -> `0.mol2'
Preparing input files

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

`REAL300000037693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037693 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [45, 15, 45, 45, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 15, 15, 45, 45, 15, 15, 15, 7, 1, 1, 5, 5, 1, 15] 65
rigid atoms, others: [33, 34, 37, 10, 11, 12, 13, 14, 15, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38])
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: REAL300000037693 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 2, 4, 4, 15, 15, 7, 7, 21, 21, 21, 21, 15, 15, 15, 15, 15, 1, 1, 5, 5, 1, 1, 2, 4, 15, 15, 21, 21, 15, 1] 65
rigid atoms, others: [1, 4, 5, 6, 7, 8, 25, 26, 38, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037693 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037693
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037693/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037693
Building REAL300000037694
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037694'
/scratch/stefan/7769618/working/building/REAL300000037694 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037694

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037694/0 /scratch/stefan/7769618/working/building/REAL300000037694 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/779
`/scratch/stefan/7769618/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1)

`REAL300000037694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037694 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 66, 66, 41, 41, 41, 36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 6, 16, 27, 27, 1, 41, 41, 66, 66, 41, 41, 6, 6, 1, 1, 1, 16, 16, 1, 41] 201
rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36])
total number of confs: 270
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037694 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 2, 2, 13, 41, 41, 41, 41, 41, 128, 170, 182, 182, 41, 1, 1, 4, 4, 1, 1, 13, 13, 41, 41, 41, 170, 170, 41, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 498
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037694 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037694/1 /scratch/stefan/7769618/working/building/REAL300000037694 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/780
`/scratch/stefan/7769618/working/3D/780' -> `1.mol2'
Preparing input files

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

`REAL300000037694.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037694/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037694 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 44, 44, 19, 19, 19, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 19, 25, 25, 1, 19, 19, 44, 44, 19, 19, 18, 6, 1, 1, 1, 19, 19, 1, 19] 201
rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36])
total number of confs: 241
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: REAL300000037694 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 6, 6, 19, 19, 19, 19, 19, 44, 74, 78, 78, 19, 1, 1, 5, 5, 1, 1, 2, 6, 19, 19, 19, 74, 74, 19, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 239
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037694 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037694
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037694/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037694/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037694
Building REAL300000037695
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037695'
/scratch/stefan/7769618/working/building/REAL300000037695 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037695

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037695/0 /scratch/stefan/7769618/working/building/REAL300000037695 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/781
`/scratch/stefan/7769618/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)C(OCC(=O)[O-])=C1)

`REAL300000037695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037695 none COC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [50, 40, 26, 40, 40, 17, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 40, 40, 84, 160, 167, 167, 40, 50, 50, 50, 40, 40, 17, 17, 1, 1, 4, 4, 1, 160, 160, 40] 201
rigid atoms, others: [33, 34, 37, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40])
total number of confs: 662
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037695 none COC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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, 5, 29, 30, 40, 40, 40, 40, 78, 78, 78, 40, 40, 1, 1, 5, 25, 44, 44, 1, 3, 3, 3, 1, 1, 5, 5, 40, 40, 78, 78, 40, 25, 25, 1] 201
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: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037695 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037695/1 /scratch/stefan/7769618/working/building/REAL300000037695 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/782
`/scratch/stefan/7769618/working/3D/782' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C(OCC(=O)[O-])=C1)

`REAL300000037695.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037695/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037695 none COC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [19, 12, 8, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 12, 12, 37, 98, 108, 108, 12, 19, 19, 19, 12, 12, 8, 2, 1, 1, 5, 5, 1, 98, 98, 12] 201
rigid atoms, others: [33, 34, 37, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40])
total number of confs: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037695 none COC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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, 12, 12, 12, 12, 12, 31, 31, 31, 12, 12, 1, 1, 7, 35, 50, 50, 1, 3, 3, 3, 1, 1, 4, 12, 12, 12, 31, 31, 12, 35, 35, 1] 201
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: 280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037695 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037695
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037695/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037695/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037695
Building REAL300000037696
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037696'
/scratch/stefan/7769618/working/building/REAL300000037696 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037696

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037696/0 /scratch/stefan/7769618/working/building/REAL300000037696 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/783
`/scratch/stefan/7769618/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)N=C1)

`REAL300000037696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037696 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 30, 45, 45, 30, 30, 30, 23, 23, 3, 1, 1, 1, 1, 1, 1, 12, 27, 27, 26, 34, 34, 1, 1, 30, 30, 45, 45, 30, 30, 3, 3, 1, 1, 1, 1, 30] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037696 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 2, 2, 15, 30, 30, 15, 29, 117, 167, 167, 167, 183, 183, 30, 30, 1, 1, 4, 4, 1, 1, 15, 15, 30, 30, 30, 30, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 598
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037696 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037696/1 /scratch/stefan/7769618/working/building/REAL300000037696 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/784
`/scratch/stefan/7769618/working/3D/784' -> `1.mol2'
Preparing input files

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

`REAL300000037696.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037696/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037696 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 17, 17, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 35, 35, 1, 1, 6, 6, 17, 17, 6, 6, 6, 4, 1, 1, 1, 1, 6] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 36])
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: REAL300000037696 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 4, 4, 6, 6, 4, 4, 25, 69, 69, 69, 69, 69, 6, 6, 1, 1, 5, 5, 1, 1, 2, 4, 6, 6, 6, 6, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 24, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037696 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037696
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037696/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037696/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037696
Building REAL300000037697
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037697'
/scratch/stefan/7769618/working/building/REAL300000037697 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037697

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037697/0 /scratch/stefan/7769618/working/building/REAL300000037697 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/785
`/scratch/stefan/7769618/working/3D/785' -> `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=C(S(N)(=O)=O)C=N2)C=C1)

`REAL300000037697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037697 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [49, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 17, 17, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 41, 41, 49, 49, 49, 41, 17, 4, 1, 1, 5, 5, 1, 41, 41] 97
rigid atoms, others: [33, 34, 37, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
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: REAL300000037697 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 31, 41, 41, 41, 41, 97, 97, 97, 41, 41, 1, 1, 3, 3, 3, 1, 11, 31, 41, 41, 97, 97, 41, 1, 1] 97
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: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037697 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037697
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037697/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037697
Building REAL300000037698
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037698'
/scratch/stefan/7769618/working/building/REAL300000037698 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037698

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037698/0 /scratch/stefan/7769618/working/building/REAL300000037698 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/786
`/scratch/stefan/7769618/working/3D/786' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1)

`REAL300000037698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037698 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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, 117, 201, 201, 117, 117, 117, 71, 71, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 117, 117, 201, 201, 117, 117, 9, 9, 1, 1, 1, 117] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
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: REAL300000037698 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 31, 117, 117, 117, 117, 117, 117, 117, 1, 1, 5, 5, 1, 1, 31, 31, 117, 117, 117, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037698 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037698/1 /scratch/stefan/7769618/working/building/REAL300000037698 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/787
`/scratch/stefan/7769618/working/3D/787' -> `1.mol2'
Preparing input files

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

`REAL300000037698.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037698/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037698 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 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, 15, 45, 45, 15, 15, 15, 14, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 45, 45, 15, 15, 14, 6, 1, 1, 1, 15] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037698 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 5, 1, 1, 4, 12, 15, 15, 15, 1] 45
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 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/7769618/working/building/REAL300000037698 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037698
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037698/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037698/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037698
Building REAL300000037699
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037699'
/scratch/stefan/7769618/working/building/REAL300000037699 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037699

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037699/0 /scratch/stefan/7769618/working/building/REAL300000037699 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/788
`/scratch/stefan/7769618/working/3D/788' -> `0.mol2'
Preparing input files

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

`REAL300000037699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037699 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 1, 7, 34, 34, 79, 79, 79, 79, 178, 178, 178, 79, 79, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 7, 79, 79, 178, 178, 79, 1, 1, 1, 1] 178
rigid atoms, others: [2, 35, 36, 37, 38, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 605
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037699 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [61, 45, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 45, 79, 79, 45, 62, 79, 79, 79, 79, 64, 64, 64, 64, 64, 45, 1, 1, 5, 5, 1, 79, 79, 79, 79] 178
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 13, 14, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 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: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037699 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037699/1 /scratch/stefan/7769618/working/building/REAL300000037699 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/789
`/scratch/stefan/7769618/working/3D/789' -> `1.mol2'
Preparing input files

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

`REAL300000037699.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037699/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037699 none CCC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 1, 7, 7, 27, 31, 31, 31, 31, 80, 80, 80, 31, 31, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 27, 31, 31, 80, 80, 31, 1, 1, 1, 1] 95
rigid atoms, others: [2, 35, 36, 37, 38, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 334
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: REAL300000037699 none CCC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [29, 19, 19, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 19, 31, 31, 19, 29, 31, 31, 31, 31, 29, 29, 29, 29, 29, 4, 1, 1, 5, 5, 1, 31, 31, 31, 31] 95
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 13, 14, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 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: 176
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037699 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037699
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037699/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037699/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037699
Building REAL300000037700
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037700'
/scratch/stefan/7769618/working/building/REAL300000037700 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037700

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037700/0 /scratch/stefan/7769618/working/building/REAL300000037700 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/790
`/scratch/stefan/7769618/working/3D/790' -> `0.mol2'
Preparing input files

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

`REAL300000037700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037700 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 21, 23, 23, 23, 23, 75, 75, 75, 23, 23, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 21, 23, 23, 75, 75, 23, 1, 1, 1, 1] 75
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: 277
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037700 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 12, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 4, 1, 1, 5, 5, 1, 23, 23, 23, 23] 75
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 52
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037700 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037700/1 /scratch/stefan/7769618/working/building/REAL300000037700 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/791
`/scratch/stefan/7769618/working/3D/791' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=CC=C1C(=O)[O-])

`REAL300000037700.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037700/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037700 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 33, 33, 61, 61, 61, 61, 139, 139, 139, 61, 61, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 61, 61, 139, 139, 61, 1, 1, 1, 1] 139
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: 448
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037700 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [31, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 31, 61, 61, 61, 61, 61, 61, 70, 70, 31, 31, 31, 31, 1, 1, 5, 5, 1, 61, 61, 61, 61] 139
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037700 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037700
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037700/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037700/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037700
Building REAL300000037701
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037701'
/scratch/stefan/7769618/working/building/REAL300000037701 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037701

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037701/0 /scratch/stefan/7769618/working/building/REAL300000037701 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/792
`/scratch/stefan/7769618/working/3D/792' -> `0.mol2'
Preparing input files

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

`REAL300000037701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037701 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
218  conformations in input
total number of sets (complete confs): 218
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 31, 31, 109, 109, 109, 31, 31, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 31, 31, 31, 109, 109, 31, 1, 1, 1, 2] 218
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 403
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: REAL300000037701 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
218  conformations in input
total number of sets (complete confs): 218
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 4, 1, 1, 5, 5, 1, 31, 31, 31, 62] 218
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36])
total number of confs: 126
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037701 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037701/1 /scratch/stefan/7769618/working/building/REAL300000037701 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/793
`/scratch/stefan/7769618/working/3D/793' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000037701.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037701/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037701 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
308  conformations in input
total number of sets (complete confs): 308
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 48, 48, 85, 85, 85, 85, 154, 154, 154, 85, 85, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 85, 85, 154, 154, 85, 1, 1, 1, 2] 308
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 485
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: REAL300000037701 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
308  conformations in input
total number of sets (complete confs): 308
using faster count positions algorithm for large data
unique positions, atoms: [37, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 37, 85, 85, 85, 85, 85, 85, 85, 85, 85, 37, 37, 37, 37, 1, 1, 5, 5, 1, 85, 85, 85, 170] 308
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36])
total number of confs: 370
number of broken/clashed sets: 129
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037701 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037701
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037701/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037701/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037701
Building REAL300000037702
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037702'
/scratch/stefan/7769618/working/building/REAL300000037702 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037702

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037702/0 /scratch/stefan/7769618/working/building/REAL300000037702 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/794
`/scratch/stefan/7769618/working/3D/794' -> `0.mol2'
Preparing input files

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

`REAL300000037702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037702 none CCC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [35, 12, 1, 12, 12, 64, 88, 88, 88, 88, 169, 169, 169, 88, 88, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 36, 36, 36, 35, 35, 64, 88, 88, 169, 169, 88, 1, 1, 1] 201
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: 701
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: REAL300000037702 none CCC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [49, 17, 17, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 17, 88, 88, 88, 88, 88, 88, 88, 88, 88, 49, 49, 49, 49, 49, 4, 1, 1, 5, 5, 1, 88, 88, 88] 201
rigid atoms, others: [32, 35, 4, 5, 6, 7, 8, 9, 13, 14, 31] set([0, 1, 2, 3, 10, 11, 12, 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: 260
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037702 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037702/1 /scratch/stefan/7769618/working/building/REAL300000037702 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/795
`/scratch/stefan/7769618/working/3D/795' -> `1.mol2'
Preparing input files

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

`REAL300000037702.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037702/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037702 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [14, 9, 1, 9, 40, 40, 84, 84, 84, 84, 201, 201, 201, 84, 84, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 9, 84, 84, 201, 201, 84, 1, 1, 1] 201
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: 700
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037702 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [47, 34, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 34, 84, 84, 84, 84, 84, 84, 84, 84, 84, 53, 53, 53, 53, 53, 34, 1, 1, 5, 5, 1, 84, 84, 84] 201
rigid atoms, others: [32, 35, 4, 5, 6, 7, 8, 9, 13, 14, 31] set([0, 1, 2, 3, 10, 11, 12, 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: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037702 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037702
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037702/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037702/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037702
Building REAL300000037703
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037703'
/scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000037703

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037703/0 /scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/796
`/scratch/stefan/7769618/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)N=C1)

`REAL300000037703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037703 none NS(=O)(=O)C1=CC=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 122, 201, 201, 122, 122, 122, 67, 66, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 122, 122, 201, 201, 122, 122, 8, 8, 1, 1, 1, 1, 122] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 35, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 628
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037703 none NS(=O)(=O)C1=CC=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 28, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 5, 5, 1, 1, 28, 28, 122, 122, 122, 122, 1] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037703/1 /scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/797
`/scratch/stefan/7769618/working/3D/797' -> `1.mol2'
Preparing input files

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

`REAL300000037703.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037703/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037703 none NS(=O)(=O)C1=CC=C(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 48, 48, 18, 18, 18, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 48, 48, 18, 18, 15, 6, 1, 1, 1, 1, 18] 48
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037703 none NS(=O)(=O)C1=CC=C(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 5, 5, 1, 1, 3, 9, 18, 18, 18, 18, 1] 48
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `2'
/scratch/stefan/7769618/working/building/REAL300000037703/2 /scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 2 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/798
`/scratch/stefan/7769618/working/3D/798' -> `2.mol2'
Preparing input files

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

`REAL300000037703.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000037703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037703/2/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: REAL300000037703 none NS(=O)(=O)C1=CC=C(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 69, 69, 21, 21, 21, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 69, 69, 21, 21, 20, 8, 1, 1, 1, 1, 21] 69
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 257
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037703 none NS(=O)(=O)C1=CC=C(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 5, 5, 1, 1, 4, 12, 21, 21, 21, 21, 1] 69
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037703 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037703
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
2: /scratch/stefan/7769618/working/building/REAL300000037703/2.*
0: /scratch/stefan/7769618/working/building/REAL300000037703/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037703/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037703
Building REAL300000037704
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037704'
/scratch/stefan/7769618/working/building/REAL300000037704 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037704

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037704/0 /scratch/stefan/7769618/working/building/REAL300000037704 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/799
`/scratch/stefan/7769618/working/3D/799' -> `0.mol2'
Preparing input files

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

`REAL300000037704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037704 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 41, 52, 52, 52, 52, 127, 127, 127, 52, 52, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 41, 52, 52, 127, 127, 52, 1, 1, 1, 1] 127
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: 468
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: REAL300000037704 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 52, 52, 52, 52, 52, 52, 52, 52, 20, 20, 20, 4, 1, 1, 5, 5, 1, 52, 52, 52, 52] 127
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 91
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037704 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037704/1 /scratch/stefan/7769618/working/building/REAL300000037704 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/800
`/scratch/stefan/7769618/working/3D/800' -> `1.mol2'
Preparing input files

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

`REAL300000037704.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037704/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037704 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 74, 74, 127, 127, 127, 127, 201, 201, 201, 127, 127, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 127, 127, 201, 201, 127, 1, 1, 1, 1] 201
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: 585
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037704 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 37, 127, 127, 127, 127, 127, 127, 127, 127, 37, 37, 37, 37, 1, 1, 5, 5, 1, 127, 127, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037704 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037704
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037704/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037704/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037704
Building REAL300000037705
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037705'
/scratch/stefan/7769618/working/building/REAL300000037705 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037705

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037705/0 /scratch/stefan/7769618/working/building/REAL300000037705 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/801
`/scratch/stefan/7769618/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1)

`REAL300000037705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037705 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [164, 92, 164, 164, 92, 92, 92, 66, 66, 9, 1, 1, 1, 1, 1, 6, 9, 9, 1, 1, 92, 92, 164, 164, 92, 92, 9, 9, 1, 6, 6, 92] 201
rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31])
total number of confs: 528
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037705 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 6, 6, 27, 92, 92, 92, 135, 136, 136, 92, 92, 1, 1, 4, 4, 1, 1, 27, 27, 92, 135, 135, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 21, 24, 25, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 402
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037705 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037705
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037705/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037705
Building REAL300000037706
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037706'
/scratch/stefan/7769618/working/building/REAL300000037706 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037706

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037706/0 /scratch/stefan/7769618/working/building/REAL300000037706 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/802
`/scratch/stefan/7769618/working/3D/802' -> `0.mol2'
Preparing input files

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

`REAL300000037706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037706 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [11, 1, 11, 11, 49, 77, 77, 77, 77, 201, 201, 201, 77, 77, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 49, 77, 77, 201, 201, 77, 1, 1, 1] 201
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: 705
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037706 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 77, 77, 77, 77, 81, 81, 77, 77, 77, 18, 18, 18, 4, 1, 1, 5, 5, 1, 77, 77, 77] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35])
total number of confs: 134
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037706 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037706/1 /scratch/stefan/7769618/working/building/REAL300000037706 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/803
`/scratch/stefan/7769618/working/3D/803' -> `1.mol2'
Preparing input files

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

`REAL300000037706.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037706/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037706 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [13, 1, 13, 55, 55, 102, 102, 102, 102, 201, 201, 201, 102, 102, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 13, 102, 102, 201, 201, 102, 1, 1, 1] 201
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: 629
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037706 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [30, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 30, 102, 102, 102, 102, 126, 126, 102, 102, 102, 30, 30, 30, 30, 1, 1, 5, 5, 1, 102, 102, 102] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35])
total number of confs: 302
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037706 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037706
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037706/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037706/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037706
Building REAL300000037707
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037707'
/scratch/stefan/7769618/working/building/REAL300000037707 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037707

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037707/0 /scratch/stefan/7769618/working/building/REAL300000037707 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/804
`/scratch/stefan/7769618/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037707 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 25, 59, 59, 25, 25, 25, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 59, 59, 25, 25, 23, 7, 1, 1, 25] 59
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: 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: REAL300000037707 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 20, 20, 25, 25, 25, 25, 25, 25, 25, 1, 1, 5, 5, 1, 1, 4, 20, 25, 25, 1] 59
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037707 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037707/1 /scratch/stefan/7769618/working/building/REAL300000037707 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/805
`/scratch/stefan/7769618/working/3D/805' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037707.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037707/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037707 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 121, 201, 201, 121, 121, 121, 65, 65, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 121, 121, 9, 9, 1, 1, 121] 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: 609
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037707 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 27, 121, 121, 121, 121, 121, 121, 121, 1, 1, 5, 5, 1, 1, 27, 27, 121, 121, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037707 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037707
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037707/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037707/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037707
Building REAL300000037708
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037708'
/scratch/stefan/7769618/working/building/REAL300000037708 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037708

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037708/0 /scratch/stefan/7769618/working/building/REAL300000037708 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/806
`/scratch/stefan/7769618/working/3D/806' -> `0.mol2'
Preparing input files

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

`REAL300000037708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037708 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 51, 15, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 51, 51, 51, 51, 137, 174, 174, 189, 180, 86, 86, 86, 51, 15, 15, 1, 1, 4, 4, 1, 51, 51, 174, 174, 174, 174] 201
rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 562
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037708 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 40, 40, 51, 51, 51, 51, 67, 67, 67, 51, 51, 1, 1, 1, 1, 7, 11, 11, 19, 17, 3, 3, 3, 1, 6, 6, 51, 51, 67, 67, 51, 1, 1, 11, 11, 11, 11] 201
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: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037708 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037708/1 /scratch/stefan/7769618/working/building/REAL300000037708 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/807
`/scratch/stefan/7769618/working/3D/807' -> `1.mol2'
Preparing input files

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

`REAL300000037708.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037708/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037708 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 15, 15, 15, 15, 52, 75, 75, 86, 84, 25, 25, 25, 15, 4, 2, 1, 1, 5, 5, 1, 15, 15, 75, 75, 75, 75] 201
rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 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: REAL300000037708 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 45, 45, 45, 15, 15, 1, 1, 1, 1, 9, 19, 21, 29, 27, 3, 3, 3, 1, 7, 15, 15, 15, 45, 45, 15, 1, 1, 19, 19, 21, 21] 201
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: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037708 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037708
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037708/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037708/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037708
Building REAL300000037709
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037709'
/scratch/stefan/7769618/working/building/REAL300000037709 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037709

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037709/0 /scratch/stefan/7769618/working/building/REAL300000037709 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/808
`/scratch/stefan/7769618/working/3D/808' -> `0.mol2'
Preparing input files

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

`REAL300000037709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037709 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 16, 51, 51, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 51, 51, 16, 16, 16, 8, 1, 1, 1, 16] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037709 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 5, 5, 1, 1, 4, 14, 16, 16, 16, 1] 51
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 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/7769618/working/building/REAL300000037709 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037709/1 /scratch/stefan/7769618/working/building/REAL300000037709 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/809
`/scratch/stefan/7769618/working/3D/809' -> `1.mol2'
Preparing input files

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

`REAL300000037709.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037709/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037709 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 103, 201, 201, 103, 103, 103, 56, 55, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 103, 103, 201, 201, 103, 103, 8, 8, 1, 1, 1, 103] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 646
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037709 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 31, 103, 103, 31, 102, 103, 103, 103, 103, 103, 1, 1, 5, 5, 1, 1, 31, 31, 103, 103, 103, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 426
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037709 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037709
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037709/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037709/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037709
Building REAL300000037710
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037710'
/scratch/stefan/7769618/working/building/REAL300000037710 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037710

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037710/0 /scratch/stefan/7769618/working/building/REAL300000037710 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/810
`/scratch/stefan/7769618/working/3D/810' -> `0.mol2'
Preparing input files

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

`REAL300000037710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037710 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 43, 66, 66, 66, 66, 175, 175, 175, 66, 66, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 43, 66, 66, 175, 175, 66, 1, 2, 2, 2, 2, 2, 2] 175
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: 638
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037710 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 66, 66, 66, 79, 79, 66, 66, 66, 66, 66, 18, 18, 18, 4, 1, 1, 5, 5, 1, 66, 66, 66, 66, 66, 66, 66] 175
rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 29, 30] set([0, 1, 2, 9, 10, 11, 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: 159
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037710 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037710/1 /scratch/stefan/7769618/working/building/REAL300000037710 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/811
`/scratch/stefan/7769618/working/3D/811' -> `1.mol2'
Preparing input files

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

`REAL300000037710.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037710/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037710 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 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: [74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 35, 6, 35, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 74, 74, 74, 74, 74, 74, 74, 35, 35, 35, 35, 1, 1, 5, 5, 1] 133
rigid atoms, others: [36, 37, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
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: REAL300000037710 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 40, 40, 74, 74, 74, 74, 133, 133, 133, 74, 74, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 74, 74, 133, 133, 74] 133
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, 39, 40])
total number of confs: 431
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037710 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037710
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037710/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037710/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037710
Building REAL300000037711
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037711'
/scratch/stefan/7769618/working/building/REAL300000037711 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037711

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037711/0 /scratch/stefan/7769618/working/building/REAL300000037711 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/812
`/scratch/stefan/7769618/working/3D/812' -> `0.mol2'
Preparing input files

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

`REAL300000037711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037711 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [51, 15, 51, 51, 15, 15, 15, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 51, 51, 15, 15, 14, 6, 1, 1, 2, 1, 15] 102
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037711 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 5, 1, 1, 4, 12, 15, 15, 30, 15, 1] 102
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037711 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037711/1 /scratch/stefan/7769618/working/building/REAL300000037711 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/813
`/scratch/stefan/7769618/working/3D/813' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1)

`REAL300000037711.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037711/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037711 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 111, 201, 201, 111, 111, 111, 62, 62, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 111, 111, 201, 201, 111, 111, 8, 8, 1, 1, 2, 1, 111] 402
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33])
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: REAL300000037711 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 27, 111, 111, 111, 111, 111, 111, 112, 112, 111, 1, 1, 5, 5, 1, 1, 27, 27, 111, 111, 222, 111, 1] 402
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 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/7769618/working/building/REAL300000037711 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037711
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037711/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037711/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037711
Building REAL300000037712
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037712'
/scratch/stefan/7769618/working/building/REAL300000037712 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037712

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037712/0 /scratch/stefan/7769618/working/building/REAL300000037712 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/814
`/scratch/stefan/7769618/working/3D/814' -> `0.mol2'
Preparing input files

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

`REAL300000037712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037712 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 23, 27, 27, 27, 27, 77, 77, 77, 27, 27, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 23, 27, 27, 77, 77, 27, 1, 1, 1, 2, 2, 2] 77
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 285
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037712 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 4, 1, 1, 5, 5, 1, 27, 27, 27, 27, 27, 27] 77
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 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: 58
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037712 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037712/1 /scratch/stefan/7769618/working/building/REAL300000037712 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/815
`/scratch/stefan/7769618/working/3D/815' -> `1.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=C(S(N)(=O)=O)C=N1)

`REAL300000037712.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037712/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037712 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 61, 30, 6, 30, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 61, 61, 61, 61, 61, 61, 30, 30, 30, 30, 1, 1, 5, 5, 1] 114
rigid atoms, others: [34, 35, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 160
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037712 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 34, 34, 61, 61, 61, 61, 114, 114, 114, 61, 61, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 61, 61, 114, 114, 61] 114
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, 37, 38])
total number of confs: 361
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037712 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037712
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037712/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037712/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037712
Building REAL300000037713
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037713'
/scratch/stefan/7769618/working/building/REAL300000037713 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037713

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037713/0 /scratch/stefan/7769618/working/building/REAL300000037713 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/816
`/scratch/stefan/7769618/working/3D/816' -> `0.mol2'
Preparing input files

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

`REAL300000037713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037713 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 84, 84, 134, 134, 134, 134, 201, 201, 201, 134, 134, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 134, 134, 201, 201, 134, 1, 1] 201
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: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037713 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 42, 134, 134, 134, 134, 134, 134, 134, 42, 42, 42, 42, 1, 1, 5, 5, 1, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 26, 27, 30] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32])
total number of confs: 264
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037713 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037713
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037713/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037713
Building REAL300000037714
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037714'
/scratch/stefan/7769618/working/building/REAL300000037714 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037714

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037714/0 /scratch/stefan/7769618/working/building/REAL300000037714 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/817
`/scratch/stefan/7769618/working/3D/817' -> `0.mol2'
Preparing input files

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

`REAL300000037714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037714 none CC(OC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [170, 126, 61, 16, 70, 70, 16, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 70, 70, 170, 177, 177, 170, 170, 170, 170, 70, 70, 16, 16, 1, 1, 4, 4, 1, 70, 70] 201
rigid atoms, others: [33, 34, 37, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 658
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037714 none CC(OC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [12, 5, 1, 1, 1, 1, 1, 1, 6, 46, 46, 70, 70, 70, 70, 109, 109, 109, 70, 70, 1, 1, 12, 16, 16, 12, 12, 12, 12, 1, 1, 6, 6, 70, 70, 109, 109, 70, 1, 1] 201
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: 377
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037714 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037714/1 /scratch/stefan/7769618/working/building/REAL300000037714 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/818
`/scratch/stefan/7769618/working/3D/818' -> `1.mol2'
Preparing input files

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

`REAL300000037714.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037714/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037714 none CC(OC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [104, 78, 24, 24, 42, 42, 13, 13, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 42, 42, 102, 106, 108, 104, 104, 104, 102, 42, 42, 13, 4, 1, 1, 5, 5, 1, 42, 42] 201
rigid atoms, others: [33, 34, 37, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 352
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037714 none CC(OC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 42, 42, 42, 96, 96, 96, 42, 42, 1, 1, 15, 24, 24, 15, 15, 15, 15, 1, 1, 6, 24, 42, 42, 96, 96, 42, 1, 1] 201
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: 408
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037714 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037714
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037714/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037714/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037714
Building REAL300000037715
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037715'
/scratch/stefan/7769618/working/building/REAL300000037715 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037715

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037715/0 /scratch/stefan/7769618/working/building/REAL300000037715 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/819
`/scratch/stefan/7769618/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C3=CC=CC=C32)N=C1)

`REAL300000037715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037715 none NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C3=CC=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 39, 39, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 39
rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 15, 16, 23, 24, 25, 26, 27, 28])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037715 none NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C3=CC=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 5, 5, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 39
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037715 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037715
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037715/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037715
Building REAL300000037716
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037716'
/scratch/stefan/7769618/working/building/REAL300000037716 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037716

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037716/0 /scratch/stefan/7769618/working/building/REAL300000037716 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/820
`/scratch/stefan/7769618/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)N=C1)

`REAL300000037716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037716 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [125, 67, 125, 125, 67, 67, 67, 58, 58, 8, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 1, 1, 1, 67, 67, 125, 125, 67, 67, 8, 8, 1, 6, 6, 1, 1, 1, 1, 67] 201
rigid atoms, others: [32, 35, 36, 37, 38, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39])
total number of confs: 419
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037716 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 2, 2, 17, 67, 67, 67, 150, 150, 150, 67, 67, 67, 67, 67, 67, 1, 1, 4, 4, 1, 1, 17, 17, 67, 150, 150, 67, 67, 67, 67, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 496
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037716 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037716
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037716/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037716
Building REAL300000037717
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037717'
/scratch/stefan/7769618/working/building/REAL300000037717 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037717

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037717/0 /scratch/stefan/7769618/working/building/REAL300000037717 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/821
`/scratch/stefan/7769618/working/3D/821' -> `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=C(S(N)(=O)=O)C=N2)N1)

`REAL300000037717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037717 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [92, 92, 92, 92, 137, 137, 92, 22, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 92, 92, 92, 92, 92, 22, 22, 1, 1, 5, 5, 1, 92] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33])
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: REAL300000037717 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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, 9, 63, 63, 92, 92, 92, 92, 201, 201, 201, 92, 92, 1, 2, 2, 2, 1, 9, 9, 92, 92, 201, 201, 92, 1] 201
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: 661
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037717 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037717/1 /scratch/stefan/7769618/working/building/REAL300000037717 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/822
`/scratch/stefan/7769618/working/3D/822' -> `1.mol2'
Preparing input files

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

`REAL300000037717.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037717/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037717 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 4, 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: [23, 23, 23, 23, 23, 23, 23, 16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 23, 23, 23, 23, 23, 16, 4, 1, 1, 5, 5, 1, 23] 72
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 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: REAL300000037717 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 19, 23, 23, 23, 23, 72, 72, 72, 23, 23, 1, 2, 2, 2, 1, 4, 18, 23, 23, 72, 72, 23, 1] 72
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: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037717 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037717
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037717/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037717/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037717
Building REAL300000037718
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037718'
/scratch/stefan/7769618/working/building/REAL300000037718 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037718

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037718/0 /scratch/stefan/7769618/working/building/REAL300000037718 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/823
`/scratch/stefan/7769618/working/3D/823' -> `0.mol2'
Preparing input files

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

`REAL300000037718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037718 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 15, 51, 51, 15, 15, 15, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 51, 51, 15, 15, 14, 6, 1, 1, 1, 1, 15] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27])
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: REAL300000037718 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 5, 1, 1, 4, 12, 15, 15, 15, 15, 1] 51
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 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/7769618/working/building/REAL300000037718 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037718/1 /scratch/stefan/7769618/working/building/REAL300000037718 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/824
`/scratch/stefan/7769618/working/3D/824' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1)

`REAL300000037718.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037718/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037718 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 119, 119, 119, 66, 66, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 119, 119, 201, 201, 119, 119, 8, 8, 1, 1, 1, 1, 119] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 614
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037718 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 29, 119, 119, 119, 119, 119, 120, 120, 119, 1, 1, 5, 5, 1, 1, 29, 29, 119, 119, 119, 119, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037718 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037718
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037718/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037718/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037718
Building REAL300000037719
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037719'
/scratch/stefan/7769618/working/building/REAL300000037719 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037719

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037719/0 /scratch/stefan/7769618/working/building/REAL300000037719 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/825
`/scratch/stefan/7769618/working/3D/825' -> `0.mol2'
Preparing input files

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

`REAL300000037719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037719 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 17, 22, 22, 22, 22, 33, 33, 33, 22, 22, 1, 1, 1, 1, 1, 1, 6, 16, 21, 35, 44, 44, 1, 5, 5, 5, 5, 22, 22, 33, 33, 22, 1, 1, 1, 16, 16, 20, 20, 35, 35, 1] 201
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: 299
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: REAL300000037719 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 22, 22, 22, 22, 22, 76, 115, 120, 161, 164, 164, 22, 9, 9, 9, 9, 1, 1, 3, 3, 1, 22, 22, 22, 115, 115, 120, 120, 161, 161, 22] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 35, 31] set([0, 1, 2, 9, 10, 11, 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: 599
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037719 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037719/1 /scratch/stefan/7769618/working/building/REAL300000037719 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/826
`/scratch/stefan/7769618/working/3D/826' -> `1.mol2'
Preparing input files

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

`REAL300000037719.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037719/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037719 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 18, 18, 18, 18, 18, 34, 34, 34, 18, 18, 1, 1, 1, 1, 1, 1, 6, 14, 18, 26, 34, 34, 1, 9, 9, 9, 18, 18, 18, 34, 34, 18, 1, 1, 1, 14, 14, 17, 17, 26, 26, 1] 201
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: 273
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: REAL300000037719 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 4, 18, 18, 18, 18, 18, 64, 84, 87, 118, 118, 118, 18, 4, 4, 4, 2, 1, 1, 4, 4, 1, 18, 18, 18, 84, 84, 87, 87, 118, 118, 18] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 35, 31] set([0, 1, 2, 9, 10, 11, 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: 390
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037719 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037719
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037719/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037719/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037719
Building REAL300000037720
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037720'
/scratch/stefan/7769618/working/building/REAL300000037720 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037720

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037720/0 /scratch/stefan/7769618/working/building/REAL300000037720 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/827
`/scratch/stefan/7769618/working/3D/827' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037720 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 44, 44, 44, 44, 44, 103, 142, 155, 155, 44, 44, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 21, 21, 21, 21, 44, 44, 44, 44, 44, 44, 142, 142, 44, 44, 1, 1, 5, 5, 1] 201
rigid atoms, others: [41, 42, 45, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 536
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037720 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 2, 1, 1, 1, 1, 1, 1, 6, 18, 32, 32, 1, 1, 7, 25, 25, 44, 44, 44, 44, 76, 76, 76, 44, 44, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 18, 18, 1, 1, 44, 44, 76, 76, 44] 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])
total number of confs: 330
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037720 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037720
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037720/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037720
Building REAL300000037721
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037721'
/scratch/stefan/7769618/working/building/REAL300000037721 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037721

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037721/0 /scratch/stefan/7769618/working/building/REAL300000037721 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/828
`/scratch/stefan/7769618/working/3D/828' -> `0.mol2'
Preparing input files

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

`REAL300000037721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037721 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [6, 1, 6, 22, 22, 35, 35, 35, 35, 61, 61, 61, 35, 35, 1, 1, 1, 1, 1, 1, 10, 20, 20, 26, 26, 1, 6, 6, 6, 6, 35, 35, 61, 61, 35, 1, 1, 1, 20, 20, 20, 20, 1] 201
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: 287
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037721 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [12, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 12, 35, 35, 35, 35, 35, 118, 159, 159, 162, 162, 35, 12, 12, 12, 12, 1, 1, 4, 4, 1, 35, 35, 35, 159, 159, 159, 159, 35] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 11, 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: 424
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037721 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037721/1 /scratch/stefan/7769618/working/building/REAL300000037721 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/829
`/scratch/stefan/7769618/working/3D/829' -> `1.mol2'
Preparing input files

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

`REAL300000037721.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037721/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037721 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [9, 1, 9, 9, 23, 23, 23, 23, 23, 58, 58, 58, 23, 23, 1, 1, 1, 1, 1, 1, 9, 20, 20, 24, 24, 1, 9, 9, 9, 23, 23, 23, 58, 58, 23, 1, 1, 1, 20, 20, 20, 20, 1] 201
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: 291
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037721 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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: [6, 6, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 6, 23, 23, 23, 23, 23, 72, 105, 105, 108, 108, 23, 6, 6, 6, 2, 1, 1, 5, 5, 1, 23, 23, 23, 105, 105, 105, 105, 23] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 11, 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: 303
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037721 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037721
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037721/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037721/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037721
Building REAL300000037722
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037722'
/scratch/stefan/7769618/working/building/REAL300000037722 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037722

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037722/0 /scratch/stefan/7769618/working/building/REAL300000037722 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/830
`/scratch/stefan/7769618/working/3D/830' -> `0.mol2'
Preparing input files

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

`REAL300000037722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037722 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 36, 41, 41, 41, 41, 95, 95, 95, 41, 41, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 36, 41, 41, 95, 95, 41, 1, 1] 95
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: 355
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037722 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 41, 41, 41, 41, 41, 41, 41, 20, 20, 20, 4, 1, 1, 5, 5, 1, 41, 41] 95
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 26, 27, 30] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32])
total number of confs: 80
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037722 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037722
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037722/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037722
Building REAL300000037723
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037723'
/scratch/stefan/7769618/working/building/REAL300000037723 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037723

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037723/0 /scratch/stefan/7769618/working/building/REAL300000037723 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/831
`/scratch/stefan/7769618/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)N=C1)

`REAL300000037723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037723 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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: [88, 29, 88, 88, 29, 29, 29, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 4, 4, 2, 4, 4, 1, 29, 29, 88, 88, 29, 29, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 29] 130
rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 16, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 39])
total number of confs: 307
number of broken/clashed sets: 130
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037723 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 53, 130, 130, 53, 53, 53, 26, 26, 4, 4, 4, 1, 4, 7, 7, 1, 1, 1, 1, 1, 1, 4, 53, 53, 130, 130, 53, 53, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 53] 130
rigid atoms, others: [32, 33, 34, 35, 36, 12, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 434
number of broken/clashed sets: 130
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037723 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 51, 51, 29, 53, 53, 50, 53, 53, 29, 1, 1, 5, 5, 1, 1, 29, 29, 29, 53, 53, 50, 53, 53, 29, 29, 1] 130
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 217
number of broken/clashed sets: 130
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037723 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037723
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037723/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037723
Building REAL300000037724
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037724'
/scratch/stefan/7769618/working/building/REAL300000037724 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037724

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037724/0 /scratch/stefan/7769618/working/building/REAL300000037724 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/832
`/scratch/stefan/7769618/working/3D/832' -> `0.mol2'
Preparing input files

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

`REAL300000037724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037724 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
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, 22, 22, 51, 51, 51, 51, 90, 90, 90, 51, 51, 1, 1, 1, 1, 1, 1, 6, 8, 8, 1, 1, 1, 4, 4, 4, 4, 51, 51, 90, 90, 51, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2] 93
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: 310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037724 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [34, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 34, 51, 51, 51, 51, 51, 60, 64, 64, 51, 51, 51, 34, 34, 34, 34, 1, 1, 5, 5, 1, 51, 51, 60, 60, 51, 51, 51, 51, 51, 51] 93
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 11, 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: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037724 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037724
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037724/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037724
Building REAL300000037725
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037725'
/scratch/stefan/7769618/working/building/REAL300000037725 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037725

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037725/0 /scratch/stefan/7769618/working/building/REAL300000037725 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/833
`/scratch/stefan/7769618/working/3D/833' -> `0.mol2'
Preparing input files

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

`REAL300000037725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037725 none CC(CCCCCCC(=O)[O-])N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [25, 6, 25, 52, 54, 63, 89, 96, 150, 163, 163, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 25, 25, 25, 25, 52, 52, 54, 54, 63, 63, 89, 89, 96, 96, 150, 150, 1, 1, 5, 5, 1] 201
rigid atoms, others: [39, 40, 43, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 780
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037725 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037725
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037725/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037725
Building REAL300000037726
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037726'
/scratch/stefan/7769618/working/building/REAL300000037726 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037726

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037726/0 /scratch/stefan/7769618/working/building/REAL300000037726 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/834
`/scratch/stefan/7769618/working/3D/834' -> `0.mol2'
Preparing input files

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

`REAL300000037726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037726 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 38, 79, 81, 81, 38, 38, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 38, 38, 38, 37, 38, 79, 79, 38, 38, 38, 38, 38, 1, 1, 5, 5, 1] 178
rigid atoms, others: [34, 35, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037726 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 1, 12, 12, 38, 38, 38, 38, 117, 117, 117, 38, 38, 2, 2, 2, 1, 1, 8, 8, 1, 1, 1, 1, 1, 38, 38, 117, 117, 38] 178
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])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037726 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037726
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037726/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037726
Building REAL300000037727
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037727'
/scratch/stefan/7769618/working/building/REAL300000037727 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037727

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037727/0 /scratch/stefan/7769618/working/building/REAL300000037727 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/835
`/scratch/stefan/7769618/working/3D/835' -> `0.mol2'
Preparing input files

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

`REAL300000037727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037727 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 81, 81, 126, 126, 126, 126, 201, 201, 201, 126, 126, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 126, 126, 201, 201, 126, 1, 1] 201
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: 604
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037727 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 39, 126, 126, 126, 126, 126, 126, 126, 39, 39, 39, 39, 1, 1, 5, 5, 1, 126, 126] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 26, 27, 30] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037727 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037727/1 /scratch/stefan/7769618/working/building/REAL300000037727 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/836
`/scratch/stefan/7769618/working/3D/836' -> `1.mol2'
Preparing input files

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

`REAL300000037727.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037727/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037727 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 33, 36, 36, 36, 36, 101, 101, 101, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 33, 36, 36, 101, 101, 36, 1, 1] 101
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: 381
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037727 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 4, 1, 1, 5, 5, 1, 36, 36] 101
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 26, 27, 30] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32])
total number of confs: 71
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037727 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037727
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037727/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037727/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037727
Building REAL300000037728
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037728'
/scratch/stefan/7769618/working/building/REAL300000037728 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037728

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037728/0 /scratch/stefan/7769618/working/building/REAL300000037728 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/837
`/scratch/stefan/7769618/working/3D/837' -> `0.mol2'
Preparing input files

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

`REAL300000037728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037728 none CC1C(N=NC2=CC=C(S(N)(=O)=O)C=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 5, 5, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 45
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 13, 14, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 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: 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: REAL300000037728 none CC1C(N=NC2=CC=C(S(N)(=O)=O)C=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 45, 45, 45, 13, 13, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 13, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 45
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 34, 15, 16, 17, 18, 35, 21, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037728 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037728
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037728/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037728
Building REAL300000037729
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037729'
/scratch/stefan/7769618/working/building/REAL300000037729 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037729

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037729/0 /scratch/stefan/7769618/working/building/REAL300000037729 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/838
`/scratch/stefan/7769618/working/3D/838' -> `0.mol2'
Preparing input files

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

`REAL300000037729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037729 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 29, 29, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 1] 52
rigid atoms, others: [34, 35, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
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: REAL300000037729 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 52, 52, 52, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 52, 52, 17] 52
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 32, 25, 26, 27, 28, 29, 30, 31] set([34, 35, 36, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 37])
total number of confs: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037729 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037729
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037729/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037729
Building REAL300000037730
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037730'
/scratch/stefan/7769618/working/building/REAL300000037730 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037730

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037730/0 /scratch/stefan/7769618/working/building/REAL300000037730 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/839
`/scratch/stefan/7769618/working/3D/839' -> `0.mol2'
Preparing input files

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

`REAL300000037730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037730 none CC1CC(N=NC2=CC=C(S(N)(=O)=O)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 1, 17, 17, 17, 17, 17] 44
rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 14, 15, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037730 none CC1CC(N=NC2=CC=C(S(N)(=O)=O)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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
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, 12, 12, 17, 17, 17, 17, 44, 44, 44, 17, 17, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 17, 17, 44, 44, 17, 1, 1, 1, 1, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 37, 19, 38, 34, 16, 17, 18, 35, 25, 26, 27, 28, 36] set([32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037730 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037730
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037730/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037730
Building REAL300000037731
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037731'
/scratch/stefan/7769618/working/building/REAL300000037731 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037731

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037731/0 /scratch/stefan/7769618/working/building/REAL300000037731 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/840
`/scratch/stefan/7769618/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)N=C1)

`REAL300000037731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037731 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 19, 40, 40, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 9, 9, 9, 9, 1, 19, 19, 40, 40, 19, 19, 1, 1, 1, 9, 9, 9, 9, 1, 1, 19] 86
rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037731 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 86, 86, 47, 47, 47, 34, 34, 9, 9, 9, 1, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 86, 86, 47, 47, 9, 9, 9, 1, 1, 1, 1, 9, 9, 47] 86
rigid atoms, others: [33, 34, 35, 36, 12, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 264
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037731 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 26, 26, 19, 47, 47, 47, 47, 47, 47, 19, 1, 1, 5, 5, 1, 1, 19, 19, 19, 47, 47, 47, 47, 19, 19, 1] 86
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 126
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037731 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037731
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037731/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037731
Building REAL300000037732
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037732'
/scratch/stefan/7769618/working/building/REAL300000037732 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037732

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037732/0 /scratch/stefan/7769618/working/building/REAL300000037732 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/841
`/scratch/stefan/7769618/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1)

`REAL300000037732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037732 none NS(=O)(=O)C1=CC=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 18, 41, 41, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 18, 18, 41, 41, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 41
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 18, 19, 23, 24, 25, 26, 27, 28])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037732 none NS(=O)(=O)C1=CC=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 5, 5, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 41
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037732 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037732/1 /scratch/stefan/7769618/working/building/REAL300000037732 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/842
`/scratch/stefan/7769618/working/3D/842' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1)

`REAL300000037732.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037732/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037732 none NS(=O)(=O)C1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 17
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 59
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: REAL300000037732 none NS(=O)(=O)C1=CC=C(NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 17
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 24
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037732 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037732
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037732/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037732/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037732
Building REAL300000037733
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037733'
/scratch/stefan/7769618/working/building/REAL300000037733 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037733

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037733/0 /scratch/stefan/7769618/working/building/REAL300000037733 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/843
`/scratch/stefan/7769618/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1)

`REAL300000037733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037733 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 121, 201, 201, 121, 121, 121, 58, 58, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 121, 121, 7, 7, 1, 1, 1, 121] 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: 592
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037733 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 25, 121, 121, 121, 121, 121, 121, 121, 1, 1, 5, 5, 1, 1, 25, 25, 121, 121, 121, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037733 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037733/1 /scratch/stefan/7769618/working/building/REAL300000037733 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/844
`/scratch/stefan/7769618/working/3D/844' -> `1.mol2'
Preparing input files

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

`REAL300000037733.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037733/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037733 none NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 13, 41, 41, 13, 13, 13, 12, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 41, 41, 13, 13, 12, 6, 1, 1, 1, 13] 41
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
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: REAL300000037733 none NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 10, 10, 13, 13, 13, 13, 13, 13, 13, 1, 1, 5, 5, 1, 1, 4, 10, 13, 13, 13, 1] 41
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 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/7769618/working/building/REAL300000037733 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037733
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037733/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037733/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037733
Building REAL300000037734
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037734'
/scratch/stefan/7769618/working/building/REAL300000037734 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037734

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037734/0 /scratch/stefan/7769618/working/building/REAL300000037734 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/845
`/scratch/stefan/7769618/working/3D/845' -> `0.mol2'
Preparing input files

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

`REAL300000037734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037734 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [19, 7, 19, 19, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 19, 19, 19, 19, 19, 19, 24, 24, 24, 24, 24, 24, 1, 1, 5, 5, 1] 35
rigid atoms, others: [34, 35, 38, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037734 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [4, 4, 1, 1, 1, 2, 2, 1, 1, 1, 4, 16, 16, 24, 24, 24, 24, 35, 35, 35, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 24, 24, 35, 35, 24] 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, 37, 38])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037734 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037734
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037734/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037734
Building REAL300000037735
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037735'
/scratch/stefan/7769618/working/building/REAL300000037735 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037735

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037735/0 /scratch/stefan/7769618/working/building/REAL300000037735 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/846
`/scratch/stefan/7769618/working/3D/846' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037735 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 14, 4, 1, 1, 5, 5, 1] 69
rigid atoms, others: [34, 35, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
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: REAL300000037735 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 23, 25, 25, 25, 25, 69, 69, 69, 25, 25, 2, 2, 2, 1, 2, 2, 2, 1, 11, 23, 25, 25, 69, 69, 25] 69
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: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037735 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037735/1 /scratch/stefan/7769618/working/building/REAL300000037735 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/847
`/scratch/stefan/7769618/working/3D/847' -> `1.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=C(S(N)(=O)=O)C=N1)

`REAL300000037735.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037735/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037735 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [106, 106, 106, 106, 106, 106, 106, 106, 106, 93, 33, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 33, 33, 1, 1, 5, 5, 1] 201
rigid atoms, others: [34, 35, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
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: REAL300000037735 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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, 2, 2, 1, 1, 1, 8, 54, 54, 106, 106, 106, 106, 201, 201, 201, 106, 106, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 106, 106, 201, 201, 106] 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])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037735 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037735
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037735/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037735/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037735
Building REAL300000037736
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037736'
/scratch/stefan/7769618/working/building/REAL300000037736 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037736

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037736/0 /scratch/stefan/7769618/working/building/REAL300000037736 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/848
`/scratch/stefan/7769618/working/3D/848' -> `0.mol2'
Preparing input files

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

`REAL300000037736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037736 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 19, 64, 64, 19, 19, 19, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 19, 19, 64, 64, 19, 19, 16, 8, 1, 1, 1, 19] 64
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037736 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 1, 1, 4, 12, 19, 19, 19, 1] 64
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037736 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037736
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037736/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037736
Building REAL300000037737
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037737'
/scratch/stefan/7769618/working/building/REAL300000037737 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037737

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037737/0 /scratch/stefan/7769618/working/building/REAL300000037737 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/849
`/scratch/stefan/7769618/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)N=C1)

`REAL300000037737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037737 none NS(=O)(=O)C1=CC=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 12, 30, 30, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12] 30
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 19, 20, 24, 25, 26, 27, 28, 29])
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: REAL300000037737 none NS(=O)(=O)C1=CC=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 30
rigid atoms, others: [1, 4, 5, 6, 7, 8, 42, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037737 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037737/1 /scratch/stefan/7769618/working/building/REAL300000037737 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/850
`/scratch/stefan/7769618/working/3D/850' -> `1.mol2'
Preparing input files

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

`REAL300000037737.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037737/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037737 none NS(=O)(=O)C1=CC=C(NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 10, 31, 31, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 31
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 42, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037737 none NS(=O)(=O)C1=CC=C(NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 5, 5, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 31
rigid atoms, others: [1, 4, 5, 6, 7, 8, 42, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037737 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037737
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037737/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037737/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037737
Building REAL300000037738
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037738'
/scratch/stefan/7769618/working/building/REAL300000037738 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037738

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037738/0 /scratch/stefan/7769618/working/building/REAL300000037738 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/851
`/scratch/stefan/7769618/working/3D/851' -> `0.mol2'
Preparing input files

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

`REAL300000037738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037738 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [17, 17, 17, 17, 17, 17, 17, 17, 13, 12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 17, 17, 17, 17, 12, 4, 1, 1, 5, 5, 1] 47
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037738 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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, 3, 3, 1, 1, 4, 4, 16, 17, 17, 17, 17, 47, 47, 47, 17, 17, 2, 2, 2, 1, 4, 16, 17, 17, 47, 47, 17] 47
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: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037738 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037738/1 /scratch/stefan/7769618/working/building/REAL300000037738 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/852
`/scratch/stefan/7769618/working/3D/852' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1)

`REAL300000037738.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037738/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037738 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [79, 79, 79, 79, 79, 79, 102, 102, 31, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 80, 80, 80, 79, 31, 31, 1, 1, 5, 5, 1] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037738 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 49, 49, 79, 79, 79, 79, 200, 200, 200, 79, 79, 2, 2, 2, 1, 7, 7, 79, 79, 201, 201, 79] 201
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: 689
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037738 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037738
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037738/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037738/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037738
Building REAL300000037739
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037739'
/scratch/stefan/7769618/working/building/REAL300000037739 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037739

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037739/0 /scratch/stefan/7769618/working/building/REAL300000037739 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/853
`/scratch/stefan/7769618/working/3D/853' -> `0.mol2'
Preparing input files

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

`REAL300000037739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037739 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 35, 97, 97, 35, 35, 35, 19, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 35, 35, 97, 97, 35, 35, 19, 7, 1, 1, 1, 35] 97
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000037739 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 5, 5, 1, 1, 4, 16, 35, 35, 35, 1] 97
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037739 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037739/1 /scratch/stefan/7769618/working/building/REAL300000037739 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/854
`/scratch/stefan/7769618/working/3D/854' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1)

`REAL300000037739.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037739/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037739 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 108, 201, 201, 108, 108, 108, 62, 62, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 108, 108, 201, 201, 108, 108, 8, 8, 1, 1, 1, 108] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 636
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037739 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 4, 22, 108, 108, 108, 108, 149, 149, 108, 108, 108, 1, 1, 5, 5, 1, 1, 22, 22, 108, 108, 108, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037739 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037739
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037739/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037739/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037739
Building REAL300000037740
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037740'
/scratch/stefan/7769618/working/building/REAL300000037740 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037740

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037740/0 /scratch/stefan/7769618/working/building/REAL300000037740 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/855
`/scratch/stefan/7769618/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037740 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [142, 84, 142, 142, 84, 84, 84, 56, 56, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 84, 84, 142, 142, 84, 84, 8, 8, 1, 1, 5, 5, 84] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 443
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037740 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 22, 84, 84, 84, 84, 155, 155, 155, 155, 84, 1, 1, 4, 4, 1, 1, 22, 22, 84, 84, 155, 155, 1] 201
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037740 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037740/1 /scratch/stefan/7769618/working/building/REAL300000037740 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/856
`/scratch/stefan/7769618/working/3D/856' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037740.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037740/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037740 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [92, 35, 92, 92, 35, 35, 35, 24, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 26, 26, 1, 35, 35, 92, 92, 35, 35, 24, 7, 1, 1, 12, 12, 35] 173
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037740 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 18, 18, 35, 35, 35, 35, 74, 74, 88, 88, 35, 1, 1, 5, 5, 1, 1, 4, 18, 35, 35, 74, 74, 1] 173
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037740 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037740
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037740/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037740/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037740
Building REAL300000037741
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037741'
/scratch/stefan/7769618/working/building/REAL300000037741 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037741

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037741/0 /scratch/stefan/7769618/working/building/REAL300000037741 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/857
`/scratch/stefan/7769618/working/3D/857' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037741 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 103, 128, 68, 68, 68, 68, 68, 68, 68, 68, 68, 36, 7, 36, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 128, 128, 128, 128, 128, 128, 128, 68, 68, 68, 36, 36, 36, 36, 1, 1, 5, 5, 1] 201
rigid atoms, others: [41, 42, 45, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 399
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: REAL300000037741 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 68, 68, 68, 68, 149, 149, 149, 68, 68, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 68, 68, 149, 149, 68] 201
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, 44, 45])
total number of confs: 510
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037741 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037741/1 /scratch/stefan/7769618/working/building/REAL300000037741 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/858
`/scratch/stefan/7769618/working/3D/858' -> `1.mol2'
Preparing input files

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

`REAL300000037741.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037741/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037741 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 59, 59, 59, 59, 158, 158, 158, 59, 59, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 19, 19, 11, 11, 11, 45, 59, 59, 158, 158, 59, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [1, 36, 37, 38, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 621
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: REAL300000037741 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 16, 59, 59, 59, 59, 59, 59, 59, 59, 59, 83, 90, 90, 16, 16, 16, 4, 1, 1, 5, 5, 1, 59, 59, 59, 90, 90, 90, 90, 90, 90, 90] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 35, 31] set([0, 1, 2, 9, 10, 11, 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: 179
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037741 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037741
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037741/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037741/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037741
Building REAL300000037742
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037742'
/scratch/stefan/7769618/working/building/REAL300000037742 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037742

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037742/0 /scratch/stefan/7769618/working/building/REAL300000037742 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/859
`/scratch/stefan/7769618/working/3D/859' -> `0.mol2'
Preparing input files

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

`REAL300000037742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037742 none NS(=O)(=O)C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 17, 17, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 8, 8, 17, 17, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8] 17
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 22, 23, 24, 25, 26, 27, 28, 36])
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: REAL300000037742 none NS(=O)(=O)C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 5, 5, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 1] 17
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037742 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037742/1 /scratch/stefan/7769618/working/building/REAL300000037742 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/860
`/scratch/stefan/7769618/working/3D/860' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1)

`REAL300000037742.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037742/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037742 none NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 67, 67, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 24, 67, 67, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 24] 67
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037742 none NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 35, 35, 24, 1, 1, 5, 5, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 1] 67
rigid atoms, others: [1, 4, 5, 6, 7, 8, 22, 23, 36, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037742 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037742
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037742/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037742/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037742
Building REAL300000037743
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037743'
/scratch/stefan/7769618/working/building/REAL300000037743 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037743

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037743/0 /scratch/stefan/7769618/working/building/REAL300000037743 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/861
`/scratch/stefan/7769618/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)N=C1)

`REAL300000037743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037743 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 62, 157, 157, 62, 62, 62, 32, 32, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 62, 62, 157, 157, 62, 62, 4, 4, 1, 1, 3, 3, 3, 3, 1, 1, 62] 201
rigid atoms, others: [34, 35, 40, 41, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037743 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 201, 201, 117, 117, 117, 63, 63, 9, 2, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 117, 117, 201, 201, 117, 117, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 117] 201
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 687
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037743 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 4, 22, 62, 62, 29, 62, 117, 117, 62, 62, 117, 117, 117, 117, 62, 62, 1, 1, 5, 5, 1, 1, 22, 22, 62, 62, 117, 117, 117, 117, 62, 62, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 42, 26, 27, 30, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037743 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037743
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037743/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037743
Building REAL300000037744
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037744'
/scratch/stefan/7769618/working/building/REAL300000037744 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037744

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037744/0 /scratch/stefan/7769618/working/building/REAL300000037744 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/862
`/scratch/stefan/7769618/working/3D/862' -> `0.mol2'
Preparing input files

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

`REAL300000037744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037744 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 38, 45, 45, 45, 45, 125, 125, 125, 45, 45, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 38, 45, 45, 125, 125, 45, 1, 1, 1] 125
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: 463
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: REAL300000037744 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 45, 45, 45, 45, 45, 45, 45, 45, 20, 20, 20, 4, 1, 1, 5, 5, 1, 45, 45, 45] 125
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34])
total number of confs: 84
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037744 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037744/1 /scratch/stefan/7769618/working/building/REAL300000037744 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/863
`/scratch/stefan/7769618/working/3D/863' -> `1.mol2'
Preparing input files

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

`REAL300000037744.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037744/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037744 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [13, 1, 13, 73, 73, 111, 111, 111, 111, 201, 201, 201, 111, 111, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 111, 111, 201, 201, 111, 1, 1, 1] 201
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: 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: REAL300000037744 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [32, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 32, 111, 111, 111, 111, 111, 111, 111, 111, 32, 32, 32, 32, 1, 1, 5, 5, 1, 111, 111, 111] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 12, 13, 27, 28, 31] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037744 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037744
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037744/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037744/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037744
Building REAL300000037745
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037745'
/scratch/stefan/7769618/working/building/REAL300000037745 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037745

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037745/0 /scratch/stefan/7769618/working/building/REAL300000037745 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/864
`/scratch/stefan/7769618/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)N=C1)

`REAL300000037745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037745 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 109, 201, 201, 109, 109, 109, 57, 56, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 109, 109, 201, 201, 109, 109, 9, 9, 1, 1, 1, 1, 1, 109] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 36])
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: REAL300000037745 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 8, 8, 31, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 1, 1, 5, 5, 1, 1, 31, 31, 109, 109, 109, 109, 109, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037745 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037745
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037745/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037745
Building REAL300000037746
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037746'
/scratch/stefan/7769618/working/building/REAL300000037746 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037746

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037746/0 /scratch/stefan/7769618/working/building/REAL300000037746 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/865
`/scratch/stefan/7769618/working/3D/865' -> `0.mol2'
Preparing input files

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

`REAL300000037746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037746 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 23, 51, 51, 23, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 51, 51, 23, 23, 23, 9, 1, 1, 1, 23] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 31])
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: REAL300000037746 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 5, 5, 1, 1, 4, 12, 23, 23, 23, 1] 51
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 21, 24, 25, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037746 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037746
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037746/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037746
Building REAL300000037747
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037747'
/scratch/stefan/7769618/working/building/REAL300000037747 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037747

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037747/0 /scratch/stefan/7769618/working/building/REAL300000037747 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/866
`/scratch/stefan/7769618/working/3D/866' -> `0.mol2'
Preparing input files

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

`REAL300000037747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037747 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [82, 32, 82, 82, 32, 32, 32, 21, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 32, 32, 82, 82, 32, 32, 21, 6, 1, 1, 2, 1, 32] 164
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33])
total number of confs: 298
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037747 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 5, 5, 1, 1, 4, 18, 32, 32, 64, 32, 1] 164
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037747 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037747/1 /scratch/stefan/7769618/working/building/REAL300000037747 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/867
`/scratch/stefan/7769618/working/3D/867' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1)

`REAL300000037747.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037747/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037747 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 111, 201, 201, 111, 111, 111, 63, 63, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 111, 111, 201, 201, 111, 111, 8, 8, 1, 1, 2, 1, 111] 402
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33])
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: REAL300000037747 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 25, 111, 111, 111, 111, 133, 133, 111, 111, 111, 1, 1, 5, 5, 1, 1, 25, 25, 111, 111, 222, 111, 1] 402
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 512
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037747 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037747
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037747/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037747/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037747
Building REAL300000037748
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037748'
/scratch/stefan/7769618/working/building/REAL300000037748 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037748

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037748/0 /scratch/stefan/7769618/working/building/REAL300000037748 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/868
`/scratch/stefan/7769618/working/3D/868' -> `0.mol2'
Preparing input files

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

`REAL300000037748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037748 none CC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 4, 1, 1, 5, 5, 1, 35] 97
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 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: REAL300000037748 none CC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 29, 35, 35, 35, 35, 97, 97, 97, 35, 35, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 11, 29, 35, 35, 97, 97, 35, 1] 97
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: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037748 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037748/1 /scratch/stefan/7769618/working/building/REAL300000037748 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/869
`/scratch/stefan/7769618/working/3D/869' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)C=C1C(=O)[O-])

`REAL300000037748.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037748/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037748 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [100, 100, 101, 101, 27, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 101, 101, 101, 144, 144, 101, 101, 101, 101, 101, 27, 27, 1, 1, 5, 5, 1, 101] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
total number of confs: 372
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037748 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 1, 9, 63, 63, 101, 101, 101, 101, 201, 201, 201, 101, 101, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 9, 101, 101, 201, 201, 101, 1] 201
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: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037748 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037748
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037748/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037748/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037748
Building REAL300000037749
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037749'
/scratch/stefan/7769618/working/building/REAL300000037749 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037749

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037749/0 /scratch/stefan/7769618/working/building/REAL300000037749 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/870
`/scratch/stefan/7769618/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)N=C1)

`REAL300000037749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037749 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 49, 125, 125, 49, 49, 49, 42, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 49, 49, 125, 125, 49, 49, 42, 8, 1, 49] 125
rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29])
total number of confs: 452
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037749 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 20, 20, 49, 49, 49, 56, 56, 49, 49, 49, 1, 1, 5, 5, 1, 1, 4, 20, 49, 1] 125
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 21, 24, 25, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037749 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037749
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037749/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037749
Building REAL300000037750
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037750'
/scratch/stefan/7769618/working/building/REAL300000037750 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037750

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037750/0 /scratch/stefan/7769618/working/building/REAL300000037750 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/871
`/scratch/stefan/7769618/working/3D/871' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037750 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [62, 62, 62, 43, 49, 62, 62, 62, 62, 43, 8, 43, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 62, 62, 62, 62, 62, 62, 43, 43, 43, 43, 1, 1, 5, 5, 1] 106
rigid atoms, others: [34, 35, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
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: REAL300000037750 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 62, 62, 62, 62, 106, 106, 106, 62, 62, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 62, 62, 106, 106, 62] 106
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, 37, 38])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037750 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037750/1 /scratch/stefan/7769618/working/building/REAL300000037750 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/872
`/scratch/stefan/7769618/working/3D/872' -> `1.mol2'
Preparing input files

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

`REAL300000037750.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037750/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037750 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 27, 35, 35, 35, 35, 75, 75, 75, 35, 35, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 27, 35, 35, 75, 75, 35, 1, 1, 1, 2, 2, 2] 75
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: 271
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037750 none CC(=NNC1=CC=C(S(N)(=O)=O)C=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 35, 35, 20, 20, 35, 35, 35, 35, 35, 20, 20, 20, 4, 1, 1, 5, 5, 1, 35, 35, 35, 35, 35, 35] 75
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 28, 29] set([0, 1, 2, 9, 10, 11, 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: 169
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037750 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037750
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037750/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037750/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037750
Building REAL300000037751
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037751'
/scratch/stefan/7769618/working/building/REAL300000037751 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037751

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037751/0 /scratch/stefan/7769618/working/building/REAL300000037751 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/873
`/scratch/stefan/7769618/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1)

`REAL300000037751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037751 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 31, 61, 61, 31, 31, 31, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 31, 31, 61, 61, 31, 31, 26, 6, 1, 1, 31] 61
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: 223
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037751 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 18, 18, 31, 31, 31, 19, 31, 31, 31, 33, 33, 1, 1, 5, 5, 1, 1, 4, 18, 31, 31, 1] 61
rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 25, 26, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037751 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037751
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037751/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037751
Building REAL300000037752
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037752'
/scratch/stefan/7769618/working/building/REAL300000037752 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037752

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037752/0 /scratch/stefan/7769618/working/building/REAL300000037752 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/874
`/scratch/stefan/7769618/working/3D/874' -> `0.mol2'
Preparing input files

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

`REAL300000037752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037752 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [22, 22, 22, 22, 22, 22, 22, 22, 16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 22, 22, 22, 22, 16, 4, 1, 1, 5, 5, 1] 57
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037752 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 22, 22, 22, 22, 57, 57, 57, 22, 22, 2, 2, 2, 1, 6, 18, 22, 22, 57, 57, 22] 57
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: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037752 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037752/1 /scratch/stefan/7769618/working/building/REAL300000037752 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/875
`/scratch/stefan/7769618/working/3D/875' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1)

`REAL300000037752.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037752/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037752 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [106, 106, 106, 106, 106, 106, 106, 106, 29, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 106, 106, 106, 106, 29, 29, 1, 1, 5, 5, 1] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31])
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: REAL300000037752 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 66, 66, 106, 106, 106, 106, 201, 201, 201, 106, 106, 2, 2, 2, 1, 9, 9, 106, 106, 201, 201, 106] 201
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: 677
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037752 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037752
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037752/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037752/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037752
Building REAL300000037753
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037753'
/scratch/stefan/7769618/working/building/REAL300000037753 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037753

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037753/0 /scratch/stefan/7769618/working/building/REAL300000037753 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/876
`/scratch/stefan/7769618/working/3D/876' -> `0.mol2'
Preparing input files

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

`REAL300000037753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037753 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [106, 106, 106, 106, 106, 106, 106, 106, 29, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 106, 106, 106, 106, 106, 29, 29, 1, 1, 5, 5, 1] 201
rigid atoms, others: [33, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 206
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037753 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 62, 62, 106, 106, 106, 106, 201, 201, 201, 106, 106, 2, 2, 2, 1, 1, 8, 8, 106, 106, 201, 201, 106] 201
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, 32, 33])
total number of confs: 676
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037753 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037753/1 /scratch/stefan/7769618/working/building/REAL300000037753 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/877
`/scratch/stefan/7769618/working/3D/877' -> `1.mol2'
Preparing input files

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

`REAL300000037753.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037753/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037753 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 24, 24, 24, 24, 24, 16, 4, 1, 1, 5, 5, 1] 59
rigid atoms, others: [33, 11, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32])
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: REAL300000037753 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 21, 24, 24, 24, 24, 59, 59, 59, 24, 24, 2, 2, 2, 1, 1, 7, 21, 24, 24, 59, 59, 24] 59
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: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037753 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037753
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037753/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037753/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037753
Building REAL300000037754
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037754'
/scratch/stefan/7769618/working/building/REAL300000037754 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037754

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037754/0 /scratch/stefan/7769618/working/building/REAL300000037754 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/878
`/scratch/stefan/7769618/working/3D/878' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037754 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 4, 1, 1, 5, 5, 1] 32
rigid atoms, others: [36, 37, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 36
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: REAL300000037754 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 11, 12, 12, 12, 12, 32, 32, 32, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 11, 12, 12, 32, 32, 12] 32
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: 127
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037754 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037754/1 /scratch/stefan/7769618/working/building/REAL300000037754 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/879
`/scratch/stefan/7769618/working/3D/879' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1)

`REAL300000037754.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037754/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037754 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 32, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 105, 32, 32, 1, 1, 5, 5, 1] 187
rigid atoms, others: [36, 37, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 217
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037754 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 49, 50, 105, 105, 105, 105, 187, 187, 187, 105, 105, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 8, 105, 105, 187, 187, 105] 187
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 11, 12, 7, 33, 31] set([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: 650
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037754 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037754
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037754/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037754/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037754
Building REAL300000037755
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037755'
/scratch/stefan/7769618/working/building/REAL300000037755 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037755

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037755/0 /scratch/stefan/7769618/working/building/REAL300000037755 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/880
`/scratch/stefan/7769618/working/3D/880' -> `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=C(S(N)(=O)=O)C=N2)O1)

`REAL300000037755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037755 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 3, 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: [35, 35, 35, 35, 35, 35, 35, 22, 22, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 35, 35, 35, 35, 35, 22, 4, 1, 1, 5, 5, 1] 91
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037755 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 26, 35, 35, 35, 35, 91, 91, 91, 35, 35, 1, 2, 2, 2, 1, 6, 26, 35, 35, 91, 91, 35] 91
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: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037755 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037755/1 /scratch/stefan/7769618/working/building/REAL300000037755 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/881
`/scratch/stefan/7769618/working/3D/881' -> `1.mol2'
Preparing input files

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

`REAL300000037755.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037755/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037755 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [100, 100, 100, 100, 124, 124, 100, 19, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 100, 101, 101, 101, 100, 19, 19, 1, 1, 5, 5, 1] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31])
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: REAL300000037755 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 66, 66, 100, 100, 100, 100, 201, 201, 201, 100, 100, 1, 2, 2, 2, 1, 8, 8, 100, 100, 201, 201, 100] 201
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: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037755 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037755
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037755/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037755/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037755
Building REAL300000037756
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037756'
/scratch/stefan/7769618/working/building/REAL300000037756 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037756

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037756/0 /scratch/stefan/7769618/working/building/REAL300000037756 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/882
`/scratch/stefan/7769618/working/3D/882' -> `0.mol2'
Preparing input files

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

`REAL300000037756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037756 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [61, 32, 32, 32, 32, 32, 37, 37, 18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 32, 61, 61, 61, 61, 61, 32, 18, 4, 1, 1, 5, 5, 1] 139
rigid atoms, others: [32, 35, 11, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
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: REAL300000037756 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 27, 32, 32, 32, 32, 73, 73, 73, 32, 32, 1, 9, 9, 9, 9, 9, 1, 5, 27, 32, 32, 73, 73, 32] 139
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: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037756 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037756
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037756/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037756
Building REAL300000037757
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037757'
/scratch/stefan/7769618/working/building/REAL300000037757 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037757

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037757/0 /scratch/stefan/7769618/working/building/REAL300000037757 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/883
`/scratch/stefan/7769618/working/3D/883' -> `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=C(S(N)(=O)=O)C=N1)

`REAL300000037757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037757 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 14, 14, 14, 14, 14, 14, 10, 4, 1, 1, 5, 5, 1] 36
rigid atoms, others: [32, 33, 36, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 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: REAL300000037757 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 36, 36, 36, 14, 14, 4, 4, 4, 1, 1, 1, 4, 14, 14, 14, 36, 36, 14] 36
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: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037757 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037757/1 /scratch/stefan/7769618/working/building/REAL300000037757 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/884
`/scratch/stefan/7769618/working/3D/884' -> `1.mol2'
Preparing input files

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

`REAL300000037757.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037757/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037757 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [142, 114, 114, 114, 114, 114, 114, 114, 114, 114, 36, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 142, 142, 142, 114, 114, 114, 36, 36, 1, 1, 5, 5, 1] 201
rigid atoms, others: [32, 33, 36, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 282
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037757 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 57, 58, 114, 114, 114, 114, 201, 201, 201, 114, 114, 3, 3, 3, 1, 1, 1, 8, 8, 114, 114, 201, 201, 114] 201
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: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037757 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037757
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037757/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037757/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037757
Building REAL300000037758
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037758'
/scratch/stefan/7769618/working/building/REAL300000037758 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037758

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037758/0 /scratch/stefan/7769618/working/building/REAL300000037758 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/885
`/scratch/stefan/7769618/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)N=C1)

`REAL300000037758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037758 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 23, 54, 54, 23, 23, 23, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 54, 54, 23, 23, 19, 6, 1, 1, 1, 1, 23] 54
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037758 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 5, 5, 1, 1, 7, 15, 23, 23, 23, 23, 1] 54
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037758 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037758
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037758/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037758
Building REAL300000037759
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037759'
/scratch/stefan/7769618/working/building/REAL300000037759 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037759

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037759/0 /scratch/stefan/7769618/working/building/REAL300000037759 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/886
`/scratch/stefan/7769618/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)N=C1)

`REAL300000037759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037759 none NS(=O)(=O)C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 23, 23, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 81
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: REAL300000037759 none NS(=O)(=O)C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 5, 5, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1] 23
rigid atoms, others: [1, 4, 5, 6, 7, 8, 38, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 28
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037759 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037759/1 /scratch/stefan/7769618/working/building/REAL300000037759 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/887
`/scratch/stefan/7769618/working/3D/887' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCCC3=NC=C(C(=O)[O-])C=C32)N=C1)

`REAL300000037759.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037759/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037759 none NS(=O)(=O)C1=CC=C(N=NC2CCCC3=NC=C(C(=O)[O-])C=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 40, 40, 21, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 40, 40, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 40
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037759 none NS(=O)(=O)C1=CC=C(N=NC2CCCC3=NC=C(C(=O)[O-])C=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 5, 5, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 40
rigid atoms, others: [1, 4, 5, 6, 7, 8, 38, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037759 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037759
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037759/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037759/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037759
Building REAL300000037760
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037760'
/scratch/stefan/7769618/working/building/REAL300000037760 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037760

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037760/0 /scratch/stefan/7769618/working/building/REAL300000037760 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/888
`/scratch/stefan/7769618/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037760 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 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, 17, 47, 47, 17, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 47, 47, 17, 17, 17, 7, 1, 1, 17] 47
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: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037760 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 1, 1, 4, 12, 17, 17, 1] 47
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037760 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037760/1 /scratch/stefan/7769618/working/building/REAL300000037760 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/889
`/scratch/stefan/7769618/working/3D/889' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037760.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037760/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037760 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 112, 201, 201, 112, 112, 112, 66, 65, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 112, 112, 201, 201, 112, 112, 8, 8, 1, 1, 112] 201
rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29])
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: REAL300000037760 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 29, 111, 111, 111, 112, 112, 111, 111, 1, 1, 5, 5, 1, 1, 29, 29, 111, 111, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037760 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037760
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037760/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037760/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037760
Building REAL300000037761
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037761'
/scratch/stefan/7769618/working/building/REAL300000037761 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037761

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037761/0 /scratch/stefan/7769618/working/building/REAL300000037761 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/890
`/scratch/stefan/7769618/working/3D/890' -> `0.mol2'
Preparing input files

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

`REAL300000037761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037761 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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, 24, 59, 59, 24, 24, 24, 24, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 24, 24, 59, 59, 24, 24, 24, 12, 1, 1, 1, 24] 59
rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 223
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037761 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 5, 5, 1, 1, 4, 16, 24, 24, 24, 1] 59
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037761 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037761
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037761/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037761
Building REAL300000037762
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037762'
/scratch/stefan/7769618/working/building/REAL300000037762 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037762

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037762/0 /scratch/stefan/7769618/working/building/REAL300000037762 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/891
`/scratch/stefan/7769618/working/3D/891' -> `0.mol2'
Preparing input files

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

`REAL300000037762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037762 none CC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 23, 13, 12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 4, 1, 1, 5, 5, 1, 23] 52
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
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: REAL300000037762 none CC1=CC=C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 23, 23, 23, 23, 52, 52, 52, 23, 23, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 20, 23, 23, 52, 52, 23, 1] 52
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: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037762 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037762/1 /scratch/stefan/7769618/working/building/REAL300000037762 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/892
`/scratch/stefan/7769618/working/3D/892' -> `1.mol2'
Preparing input files

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

`REAL300000037762.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037762/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037762 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [81, 81, 81, 81, 28, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 28, 28, 1, 1, 5, 5, 1, 81] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
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: REAL300000037762 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 1, 8, 45, 46, 81, 81, 81, 81, 201, 201, 201, 81, 81, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 8, 8, 81, 81, 201, 201, 81, 1] 201
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: 681
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037762 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037762
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037762/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037762/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037762
Building REAL300000037763
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037763'
/scratch/stefan/7769618/working/building/REAL300000037763 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037763

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037763/0 /scratch/stefan/7769618/working/building/REAL300000037763 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/893
`/scratch/stefan/7769618/working/3D/893' -> `0.mol2'
Preparing input files

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

`REAL300000037763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037763 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [77, 61, 61, 61, 19, 19, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 61, 61, 61, 61, 98, 98, 77, 77, 77, 61, 19, 4, 1, 1, 5, 5, 1, 61, 61] 186
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36])
total number of confs: 281
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037763 none COC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 35, 61, 61, 61, 61, 171, 171, 171, 61, 61, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 10, 35, 61, 61, 171, 171, 61, 1, 1] 186
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: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037763 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037763/1 /scratch/stefan/7769618/working/building/REAL300000037763 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/894
`/scratch/stefan/7769618/working/3D/894' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=CC=C1C(=O)[O-])

`REAL300000037763.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037763/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037763 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 77, 77, 77, 17, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 77, 77, 77, 77, 118, 118, 118, 118, 118, 77, 17, 17, 1, 1, 4, 4, 1, 77, 77] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36])
total number of confs: 386
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037763 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 46, 46, 77, 77, 77, 77, 132, 132, 132, 77, 77, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 6, 6, 77, 77, 132, 132, 77, 1, 1] 201
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: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037763 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037763
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037763/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037763/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037763
Building REAL300000037764
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037764'
/scratch/stefan/7769618/working/building/REAL300000037764 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037764

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037764/0 /scratch/stefan/7769618/working/building/REAL300000037764 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/895
`/scratch/stefan/7769618/working/3D/895' -> `0.mol2'
Preparing input files

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

`REAL300000037764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037764 none NS(=O)(=O)C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 17, 45, 45, 17, 17, 17, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 45, 45, 17, 17, 16, 6, 1, 1, 17] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 32, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037764 none NS(=O)(=O)C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 14, 14, 16, 16, 16, 14, 14, 16, 16, 16, 16, 16, 1, 1, 5, 5, 1, 1, 4, 14, 16, 16, 1] 45
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 22, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 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/7769618/working/building/REAL300000037764 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037764
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037764/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037764
Building REAL300000037765
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037765'
/scratch/stefan/7769618/working/building/REAL300000037765 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037765

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037765/0 /scratch/stefan/7769618/working/building/REAL300000037765 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/896
`/scratch/stefan/7769618/working/3D/896' -> `0.mol2'
Preparing input files

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

`REAL300000037765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037765 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [113, 113, 113, 113, 134, 134, 113, 23, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 113, 113, 113, 113, 113, 23, 23, 1, 1, 5, 5, 1, 113] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33])
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: REAL300000037765 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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, 3, 3, 1, 1, 1, 9, 72, 72, 113, 113, 113, 113, 201, 201, 201, 113, 113, 1, 2, 2, 2, 1, 9, 9, 113, 113, 201, 201, 113, 1] 201
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: 629
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037765 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037765/1 /scratch/stefan/7769618/working/building/REAL300000037765 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/897
`/scratch/stefan/7769618/working/3D/897' -> `1.mol2'
Preparing input files

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

`REAL300000037765.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037765/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037765 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 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: [38, 38, 38, 38, 38, 38, 38, 19, 19, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 38, 38, 38, 38, 38, 19, 4, 1, 1, 5, 5, 1, 38] 94
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037765 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 34, 38, 38, 38, 38, 94, 94, 94, 38, 38, 1, 2, 2, 2, 1, 7, 34, 38, 38, 94, 94, 38, 1] 94
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: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037765 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037765
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037765/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037765/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037765
Building REAL300000037766
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037766'
/scratch/stefan/7769618/working/building/REAL300000037766 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037766

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037766/0 /scratch/stefan/7769618/working/building/REAL300000037766 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/898
`/scratch/stefan/7769618/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)N=C1)

`REAL300000037766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037766 none NS(=O)(=O)C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [60, 21, 60, 60, 21, 21, 21, 19, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 21, 21, 60, 60, 21, 21, 19, 9, 2, 1, 1, 1, 1, 1, 21] 120
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037766 none NS(=O)(=O)C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 5, 5, 1, 1, 4, 12, 42, 21, 21, 21, 21, 21, 1] 120
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037766 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037766
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037766/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037766
Building REAL300000037767
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037767'
/scratch/stefan/7769618/working/building/REAL300000037767 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037767

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037767/0 /scratch/stefan/7769618/working/building/REAL300000037767 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/899
`/scratch/stefan/7769618/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=C(Cl)S2)N=C1)

`REAL300000037767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037767 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=C(Cl)S2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 22, 53, 53, 22, 22, 22, 18, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 22, 22, 53, 53, 22, 22, 18, 6, 1, 22] 53
rigid atoms, others: [10, 11, 12, 13, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037767 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=C(Cl)S2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 22, 22, 24, 24, 22, 22, 22, 22, 1, 1, 5, 5, 1, 1, 4, 16, 22, 1] 53
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 21, 24, 25, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037767 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037767
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037767/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037767
Building REAL300000037768
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037768'
/scratch/stefan/7769618/working/building/REAL300000037768 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037768

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037768/0 /scratch/stefan/7769618/working/building/REAL300000037768 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/900
`/scratch/stefan/7769618/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1)

`REAL300000037768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037768 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 22, 53, 53, 22, 22, 22, 18, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 22, 22, 53, 53, 22, 22, 18, 6, 1, 1, 22] 53
rigid atoms, others: [10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037768 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 22, 22, 24, 24, 22, 22, 22, 1, 1, 5, 5, 1, 1, 4, 16, 22, 22, 1] 53
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037768 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037768
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037768/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037768
Building REAL300000037769
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037769'
/scratch/stefan/7769618/working/building/REAL300000037769 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037769

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037769/0 /scratch/stefan/7769618/working/building/REAL300000037769 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/901
`/scratch/stefan/7769618/working/3D/901' -> `0.mol2'
Preparing input files

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

`REAL300000037769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037769 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 21, 53, 53, 21, 21, 21, 18, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 53, 53, 21, 21, 18, 6, 1, 1, 21] 53
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037769 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 21, 21, 21, 21, 21, 21, 21, 1, 1, 5, 5, 1, 1, 4, 16, 21, 21, 1] 53
rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037769 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037769
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037769/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037769
Building REAL300000037770
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037770'
/scratch/stefan/7769618/working/building/REAL300000037770 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037770

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037770/0 /scratch/stefan/7769618/working/building/REAL300000037770 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/902
`/scratch/stefan/7769618/working/3D/902' -> `0.mol2'
Preparing input files

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

`REAL300000037770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037770 none CCOC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens 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, 39, 39, 39, 10, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 39, 39, 39, 39, 141, 165, 165, 165, 74, 74, 74, 74, 74, 39, 10, 10, 1, 1, 4, 4, 1, 39, 39, 165, 165] 201
rigid atoms, others: [35, 36, 39, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 40, 41, 42, 43])
total number of confs: 436
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037770 none CCOC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 6, 34, 34, 39, 39, 39, 39, 57, 57, 57, 39, 39, 1, 1, 1, 1, 7, 16, 18, 18, 3, 3, 3, 3, 3, 1, 6, 6, 39, 39, 57, 57, 39, 1, 1, 16, 16] 201
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: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037770 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037770/1 /scratch/stefan/7769618/working/building/REAL300000037770 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/903
`/scratch/stefan/7769618/working/3D/903' -> `1.mol2'
Preparing input files

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

`REAL300000037770.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037770/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037770 none CCOC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 31, 13, 13, 13, 4, 4, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 44, 86, 90, 90, 39, 39, 39, 39, 39, 13, 4, 2, 1, 1, 4, 4, 1, 13, 13, 86, 86] 201
rigid atoms, others: [35, 36, 39, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 40, 41, 42, 43])
total number of confs: 372
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037770 none CCOC1=CC(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 31, 31, 31, 13, 13, 1, 1, 1, 1, 7, 25, 37, 37, 13, 13, 13, 13, 13, 1, 7, 13, 13, 13, 31, 31, 13, 1, 1, 25, 25] 201
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: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037770 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037770
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037770/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037770/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037770
Building REAL300000037771
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037771'
/scratch/stefan/7769618/working/building/REAL300000037771 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037771

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037771/0 /scratch/stefan/7769618/working/building/REAL300000037771 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/904
`/scratch/stefan/7769618/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])N=C1)

`REAL300000037771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037771 none NS(=O)(=O)C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [69, 27, 69, 69, 27, 27, 27, 20, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 27, 27, 69, 69, 27, 27, 20, 4, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27] 177
rigid atoms, others: [33, 10, 11, 12, 13, 14, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 265
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037771 none NS(=O)(=O)C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 70, 177, 177, 70, 70, 70, 65, 27, 27, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 20, 70, 70, 177, 177, 70, 70, 65, 27, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70] 177
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43])
total number of confs: 676
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037771 none NS(=O)(=O)C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 19, 19, 27, 27, 27, 70, 70, 70, 70, 70, 27, 27, 27, 30, 30, 1, 1, 5, 5, 1, 1, 5, 19, 27, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1] 177
rigid atoms, others: [1, 4, 5, 6, 7, 8, 43, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037771 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037771
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037771/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037771
Building REAL300000037772
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037772'
/scratch/stefan/7769618/working/building/REAL300000037772 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037772

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037772/0 /scratch/stefan/7769618/working/building/REAL300000037772 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/905
`/scratch/stefan/7769618/working/3D/905' -> `0.mol2'
Preparing input files

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

`REAL300000037772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037772 none COC1=CC=C(C)C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [32, 26, 26, 26, 26, 26, 26, 15, 15, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 26, 26, 30, 30, 32, 32, 32, 26, 26, 26, 26, 26, 15, 4, 1, 1, 5, 5, 1] 64
rigid atoms, others: [35, 36, 39, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
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: REAL300000037772 none COC1=CC=C(C)C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 26, 26, 26, 26, 56, 56, 56, 26, 26, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 7, 18, 26, 26, 56, 56, 26] 64
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: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037772 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037772
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037772/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037772
Building REAL300000037773
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037773'
/scratch/stefan/7769618/working/building/REAL300000037773 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037773

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037773/0 /scratch/stefan/7769618/working/building/REAL300000037773 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/906
`/scratch/stefan/7769618/working/3D/906' -> `0.mol2'
Preparing input files

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

`REAL300000037773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037773 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 4, 1, 1, 5, 5, 1] 59
rigid atoms, others: [35, 36, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
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: REAL300000037773 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 18, 18, 18, 18, 59, 59, 59, 18, 18, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 16, 18, 18, 59, 59, 18] 59
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: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037773 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037773/1 /scratch/stefan/7769618/working/building/REAL300000037773 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/907
`/scratch/stefan/7769618/working/3D/907' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(CN=NC2=CC=C(S(N)(=O)=O)C=N2)=C1C(=O)[O-])

`REAL300000037773.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037773/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037773 none CN1C2=CC=C(F)C=C2C(CN=NC2=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [78, 78, 78, 78, 78, 78, 78, 78, 78, 30, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 78, 78, 86, 86, 78, 78, 78, 78, 78, 78, 30, 30, 1, 1, 5, 5, 1] 201
rigid atoms, others: [35, 36, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
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: REAL300000037773 none CN1C2=CC=C(F)C=C2C(CN=NC2=CC=C(S(N)(=O)=O)C=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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, 1, 1, 1, 1, 1, 8, 48, 48, 78, 78, 78, 78, 201, 201, 201, 78, 78, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 8, 8, 78, 78, 201, 201, 78] 201
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: 674
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037773 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037773
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037773/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037773/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037773
Building REAL300000037774
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037774'
/scratch/stefan/7769618/working/building/REAL300000037774 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037774

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037774/0 /scratch/stefan/7769618/working/building/REAL300000037774 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/908
`/scratch/stefan/7769618/working/3D/908' -> `0.mol2'
Preparing input files

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

`REAL300000037774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037774 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [9, 1, 9, 47, 47, 85, 85, 85, 85, 201, 201, 201, 85, 85, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 85, 85, 201, 201, 85, 1, 1, 1, 1] 201
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: 662
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037774 none CC(N=NC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [36, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 36, 85, 85, 119, 119, 85, 85, 85, 85, 85, 85, 85, 36, 36, 36, 36, 1, 1, 5, 5, 1, 85, 85, 85, 85] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 11, 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: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037774 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037774/1 /scratch/stefan/7769618/working/building/REAL300000037774 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/909
`/scratch/stefan/7769618/working/3D/909' -> `1.mol2'
Preparing input files

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

`REAL300000037774.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037774/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037774 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 36, 47, 47, 47, 47, 123, 123, 123, 47, 47, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 47, 47, 123, 123, 47, 1, 1, 1, 1] 123
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: 447
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037774 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 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
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 47, 47, 49, 49, 47, 47, 47, 47, 47, 47, 47, 18, 18, 18, 4, 1, 1, 5, 5, 1, 47, 47, 47, 47] 123
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 30, 31] set([0, 1, 2, 9, 10, 11, 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: 92
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037774 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037774
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037774/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037774/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037774
Building REAL300000037775
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037775'
/scratch/stefan/7769618/working/building/REAL300000037775 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037775

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037775/0 /scratch/stefan/7769618/working/building/REAL300000037775 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/910
`/scratch/stefan/7769618/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037775 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [136, 71, 136, 136, 71, 71, 71, 46, 46, 7, 1, 1, 1, 1, 1, 1, 7, 9, 15, 12, 1, 71, 71, 136, 136, 71, 71, 7, 7, 1, 1, 7, 7, 9, 9, 71] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 487
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037775 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 2, 2, 16, 71, 71, 71, 71, 111, 141, 150, 148, 71, 1, 1, 5, 5, 1, 1, 16, 16, 71, 71, 111, 111, 141, 141, 1] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037775 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037775/1 /scratch/stefan/7769618/working/building/REAL300000037775 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/911
`/scratch/stefan/7769618/working/3D/911' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037775.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037775/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037775 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [83, 29, 83, 83, 29, 29, 29, 19, 7, 7, 1, 1, 1, 1, 1, 1, 8, 20, 31, 23, 1, 29, 29, 83, 83, 29, 29, 19, 7, 1, 1, 8, 8, 20, 20, 29] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 412
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037775 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 29, 29, 29, 29, 60, 77, 80, 79, 29, 1, 1, 5, 5, 1, 1, 4, 16, 29, 29, 60, 60, 77, 77, 1] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037775 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037775
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037775/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037775/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037775
Building REAL300000037776
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037776'
/scratch/stefan/7769618/working/building/REAL300000037776 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037776

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037776/0 /scratch/stefan/7769618/working/building/REAL300000037776 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/912
`/scratch/stefan/7769618/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)N=C1)

`REAL300000037776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037776 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 201, 201, 117, 117, 117, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 117, 117, 201, 201, 117, 117, 8, 8, 1, 1, 1, 1, 1, 117] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 605
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037776 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 27, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 5, 5, 1, 1, 27, 27, 117, 117, 117, 117, 117, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037776 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037776
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037776/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037776
Building REAL300000037777
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037777'
/scratch/stefan/7769618/working/building/REAL300000037777 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037777

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037777/0 /scratch/stefan/7769618/working/building/REAL300000037777 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/913
`/scratch/stefan/7769618/working/3D/913' -> `0.mol2'
Preparing input files

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

`REAL300000037777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037777 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 25, 28, 28, 28, 28, 62, 62, 62, 28, 28, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 28, 28, 62, 62, 28, 1, 1, 1, 1, 1] 62
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: 223
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037777 none CC(=NNC1=CC=C(S(N)(=O)=O)C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 4, 1, 1, 5, 5, 1, 28, 28, 28, 28, 28] 62
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 35, 31] set([0, 1, 2, 9, 10, 11, 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: 59
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037777 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037777/1 /scratch/stefan/7769618/working/building/REAL300000037777 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/914
`/scratch/stefan/7769618/working/3D/914' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000037777.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037777/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037777 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 33, 33, 53, 53, 53, 53, 118, 118, 118, 53, 53, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 53, 53, 118, 118, 53, 1, 1, 1, 1, 1] 118
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: 372
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037777 none CC(N=NC1=CC=C(S(N)(=O)=O)C=N1)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [30, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 30, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 30, 30, 30, 30, 1, 1, 5, 5, 1, 53, 53, 53, 53, 53] 118
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 35, 31] set([0, 1, 2, 9, 10, 11, 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: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037777 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037777
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037777/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037777/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037777
Building REAL300000037778
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037778'
/scratch/stefan/7769618/working/building/REAL300000037778 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037778

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037778/0 /scratch/stefan/7769618/working/building/REAL300000037778 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/915
`/scratch/stefan/7769618/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1)

`REAL300000037778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037778 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 124, 201, 201, 124, 124, 124, 68, 68, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 124, 124, 201, 201, 124, 124, 8, 8, 1, 1, 1, 1, 124] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 612
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037778 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 29, 124, 124, 124, 124, 124, 124, 125, 125, 124, 124, 124, 1, 1, 5, 5, 1, 1, 29, 29, 124, 124, 124, 124, 1] 201
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037778 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037778/1 /scratch/stefan/7769618/working/building/REAL300000037778 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/916
`/scratch/stefan/7769618/working/3D/916' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1)

`REAL300000037778.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037778/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037778 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 25, 65, 65, 25, 25, 25, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 65, 65, 25, 25, 23, 7, 1, 1, 1, 1, 25] 65
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037778 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 18, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 5, 5, 1, 1, 4, 18, 25, 25, 25, 25, 1] 65
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037778 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037778
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037778/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037778/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037778
Building REAL300000037779
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037779'
/scratch/stefan/7769618/working/building/REAL300000037779 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037779

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037779/0 /scratch/stefan/7769618/working/building/REAL300000037779 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/917
`/scratch/stefan/7769618/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)N=C1)

`REAL300000037779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037779 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 15, 48, 48, 15, 15, 15, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 48, 48, 15, 15, 14, 4, 1, 1, 1, 1, 15] 48
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037779 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 5, 1, 1, 4, 12, 15, 15, 15, 15, 1] 48
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037779 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037779
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037779/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037779
Building REAL300000037780
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037780'
/scratch/stefan/7769618/working/building/REAL300000037780 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037780

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037780/0 /scratch/stefan/7769618/working/building/REAL300000037780 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/918
`/scratch/stefan/7769618/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1)

`REAL300000037780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037780 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 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]
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, 18, 42, 42, 18, 18, 18, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 18, 42, 42, 18, 18, 17, 5, 1, 1, 1, 18] 42
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, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037780 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 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]
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, 1, 1, 1, 1, 1, 4, 12, 12, 18, 18, 17, 18, 18, 18, 18, 18, 18, 1, 1, 5, 5, 1, 1, 4, 12, 18, 18, 18, 1] 42
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 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/7769618/working/building/REAL300000037780 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037780
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037780/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037780
Building REAL300000037781
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037781'
/scratch/stefan/7769618/working/building/REAL300000037781 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037781

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037781/0 /scratch/stefan/7769618/working/building/REAL300000037781 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/919
`/scratch/stefan/7769618/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(Br)=C2C(=O)[O-])N=C1)

`REAL300000037781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037781 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(Br)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 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]
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, 17, 41, 41, 17, 17, 17, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 41, 41, 17, 17, 16, 4, 1, 1, 1, 17] 41
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, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
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: REAL300000037781 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(Br)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 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]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 14, 14, 17, 17, 16, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 1, 1, 4, 14, 17, 17, 17, 1] 41
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037781 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037781
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037781/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037781
Building REAL300000037782
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037782'
/scratch/stefan/7769618/working/building/REAL300000037782 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037782

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037782/0 /scratch/stefan/7769618/working/building/REAL300000037782 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/920
`/scratch/stefan/7769618/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)N=C1)

`REAL300000037782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037782 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 32, 73, 73, 32, 32, 32, 28, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 32, 32, 73, 73, 32, 32, 28, 7, 1, 1, 1, 1, 32] 73
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 35, 23, 24, 25, 26, 27, 28, 29, 30])
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: REAL300000037782 none NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 21, 21, 32, 32, 33, 33, 32, 32, 32, 32, 32, 32, 32, 1, 1, 5, 5, 1, 1, 4, 21, 32, 32, 32, 32, 1] 73
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 23, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037782 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037782
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037782/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037782
Building REAL300000037783
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037783'
/scratch/stefan/7769618/working/building/REAL300000037783 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037783

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037783/0 /scratch/stefan/7769618/working/building/REAL300000037783 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/921
`/scratch/stefan/7769618/working/3D/921' -> `0.mol2'
Preparing input files

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

`REAL300000037783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037783 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 16, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 20, 20, 16, 4, 1, 1, 5, 5, 1, 20] 52
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 33])
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: REAL300000037783 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 18, 20, 20, 20, 20, 52, 52, 52, 20, 20, 1, 1, 1, 6, 18, 20, 20, 52, 52, 20, 1] 52
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: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037783 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037783
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037783/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037783
Building REAL300000037784
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037784'
/scratch/stefan/7769618/working/building/REAL300000037784 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037784

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037784/0 /scratch/stefan/7769618/working/building/REAL300000037784 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/922
`/scratch/stefan/7769618/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)N=C1)

`REAL300000037784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037784 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 72, 118, 118, 72, 72, 72, 42, 42, 6, 1, 1, 1, 1, 1, 1, 7, 17, 19, 19, 1, 1, 1, 72, 72, 118, 118, 72, 72, 6, 6, 1, 1, 17, 17, 1, 72] 201
rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 439
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037784 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 2, 2, 16, 72, 72, 72, 72, 140, 190, 192, 192, 72, 72, 72, 1, 1, 4, 4, 1, 1, 16, 16, 72, 72, 190, 190, 72, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037784 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037784/1 /scratch/stefan/7769618/working/building/REAL300000037784 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/923
`/scratch/stefan/7769618/working/3D/923' -> `1.mol2'
Preparing input files

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

`REAL300000037784.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037784/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037784 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 58, 58, 24, 24, 24, 15, 7, 7, 1, 1, 1, 1, 1, 1, 7, 29, 43, 43, 1, 1, 1, 24, 24, 58, 58, 24, 24, 15, 7, 1, 1, 29, 29, 1, 24] 201
rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 345
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037784 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 10, 10, 24, 24, 15, 24, 62, 94, 97, 97, 24, 24, 24, 1, 1, 5, 5, 1, 1, 4, 10, 24, 24, 94, 94, 24, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 23, 24, 36, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037784 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037784
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037784/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037784/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037784
Building REAL300000037785
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037785'
/scratch/stefan/7769618/working/building/REAL300000037785 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037785

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037785/0 /scratch/stefan/7769618/working/building/REAL300000037785 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/924
`/scratch/stefan/7769618/working/3D/924' -> `0.mol2'
Preparing input files

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

`REAL300000037785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037785 none CC1=NSC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 18, 18, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 24, 24, 24, 24, 24, 24, 24, 18, 4, 1, 1, 5, 5, 1] 55
rigid atoms, others: [7, 8, 9, 10, 11, 12, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
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: REAL300000037785 none CC1=NSC(C=NNC2=CC=C(S(N)(=O)=O)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 20, 24, 24, 24, 24, 55, 55, 55, 24, 24, 1, 1, 3, 3, 2, 2, 2, 4, 20, 24, 24, 55, 55, 24] 55
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: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037785 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037785
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037785/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037785
Building REAL300000037786
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037786'
/scratch/stefan/7769618/working/building/REAL300000037786 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037786

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037786/0 /scratch/stefan/7769618/working/building/REAL300000037786 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/925
`/scratch/stefan/7769618/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)N=C1)

`REAL300000037786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037786 none NS(=O)(=O)C1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 28, 64, 64, 28, 28, 28, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 64, 64, 28, 28, 26, 10, 1, 1, 1, 28] 64
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 225
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: REAL300000037786 none NS(=O)(=O)C1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 5, 5, 1, 1, 4, 12, 28, 28, 28, 1] 64
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 56
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037786 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037786
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037786/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037786
Building REAL300000037787
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037787'
/scratch/stefan/7769618/working/building/REAL300000037787 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037787

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037787/0 /scratch/stefan/7769618/working/building/REAL300000037787 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/926
`/scratch/stefan/7769618/working/3D/926' -> `0.mol2'
Preparing input files

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

`REAL300000037787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037787 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 20, 20, 20, 20, 20, 12, 4, 1, 1, 5, 5, 1] 58
rigid atoms, others: [32, 33, 36, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
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: REAL300000037787 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 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, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 20, 20, 20, 20, 58, 58, 58, 20, 20, 3, 3, 3, 1, 1, 1, 8, 18, 20, 20, 58, 58, 20] 58
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: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037787 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037787/1 /scratch/stefan/7769618/working/building/REAL300000037787 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/927
`/scratch/stefan/7769618/working/3D/927' -> `1.mol2'
Preparing input files

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

`REAL300000037787.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037787/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037787 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [123, 107, 107, 107, 106, 107, 107, 107, 107, 107, 27, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 123, 123, 123, 107, 107, 107, 27, 27, 1, 1, 5, 5, 1] 201
rigid atoms, others: [32, 33, 36, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 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: REAL300000037787 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(N)(=O)=O)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 57, 58, 107, 107, 107, 107, 201, 201, 201, 107, 107, 4, 4, 4, 1, 1, 1, 8, 8, 107, 107, 201, 201, 107] 201
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: 657
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037787 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037787
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037787/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037787/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037787
Building REAL300000037788
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037788'
/scratch/stefan/7769618/working/building/REAL300000037788 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037788

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037788/0 /scratch/stefan/7769618/working/building/REAL300000037788 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/928
`/scratch/stefan/7769618/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1)

`REAL300000037788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 70, 138, 138, 70, 70, 70, 44, 44, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 8, 1, 1, 70, 70, 138, 138, 70, 70, 6, 6, 8, 8, 8, 8, 1, 1, 70] 201
rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 462
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 114, 201, 201, 114, 114, 114, 92, 92, 22, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 8, 8, 114, 114, 201, 201, 114, 114, 22, 22, 1, 1, 1, 1, 8, 8, 114] 201
rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 6, 6, 25, 70, 70, 70, 114, 114, 114, 114, 114, 154, 154, 114, 70, 70, 1, 1, 5, 5, 1, 1, 25, 25, 114, 114, 114, 114, 70, 70, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037788 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037788/1 /scratch/stefan/7769618/working/building/REAL300000037788 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/929
`/scratch/stefan/7769618/working/3D/929' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1)

`REAL300000037788.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037788/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 78, 78, 31, 31, 31, 21, 7, 7, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 11, 1, 1, 31, 31, 78, 78, 31, 31, 21, 7, 11, 11, 11, 11, 1, 1, 31] 201
rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 82, 201, 201, 82, 82, 82, 68, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 82, 82, 201, 201, 82, 82, 68, 35, 1, 1, 1, 1, 11, 11, 82] 201
rigid atoms, others: [33, 34, 35, 36, 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, 37, 38, 39])
total number of confs: 745
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037788 none NS(=O)(=O)C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)N=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 4, 16, 16, 31, 31, 31, 82, 82, 82, 82, 82, 84, 84, 82, 31, 31, 1, 1, 5, 5, 1, 1, 4, 16, 82, 82, 82, 82, 31, 31, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 25, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037788 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037788
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037788/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037788/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037788
Building REAL300000037789
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037789'
/scratch/stefan/7769618/working/building/REAL300000037789 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037789

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037789/0 /scratch/stefan/7769618/working/building/REAL300000037789 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/930
`/scratch/stefan/7769618/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1)

`REAL300000037789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037789 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 121, 73, 121, 121, 73, 73, 73, 35, 35, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 4, 4, 1, 1, 1, 1, 73] 201
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037789 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 49, 73, 74, 51, 74, 74, 74, 74, 74, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 49, 49, 73, 74, 74, 74, 1] 201
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037789 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037789/1 /scratch/stefan/7769618/working/building/REAL300000037789 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/931
`/scratch/stefan/7769618/working/3D/931' -> `1.mol2'
Preparing input files

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

`REAL300000037789.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037789/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037789 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 5, 8, 8, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 3, 3, 1, 1, 1, 1, 5] 14
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 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: REAL300000037789 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 3, 5, 5, 5, 5, 5, 1] 14
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037789 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037789
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037789/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037789/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037789
Building REAL300000037790
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037790'
/scratch/stefan/7769618/working/building/REAL300000037790 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037790

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037790/0 /scratch/stefan/7769618/working/building/REAL300000037790 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/932
`/scratch/stefan/7769618/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037790 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 9, 11, 11, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 5, 1, 1, 1, 1, 9] 19
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: 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: REAL300000037790 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 2, 4, 9, 9, 9, 9, 1] 19
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037790 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037790/1 /scratch/stefan/7769618/working/building/REAL300000037790 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/933
`/scratch/stefan/7769618/working/3D/933' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037790.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037790/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037790 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 157, 98, 65, 98, 98, 65, 65, 65, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 65, 65, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 65, 65, 6, 6, 1, 1, 1, 1, 65] 157
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: 544
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037790 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 24, 65, 65, 65, 65, 65, 65, 67, 67, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 24, 24, 65, 65, 65, 65, 1] 157
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037790 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037790
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037790/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037790/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037790
Building REAL300000037791
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037791'
/scratch/stefan/7769618/working/building/REAL300000037791 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037791

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037791/0 /scratch/stefan/7769618/working/building/REAL300000037791 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/934
`/scratch/stefan/7769618/working/3D/934' -> `0.mol2'
Preparing input files

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

`REAL300000037791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037791 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 22, 22, 36, 36, 36, 36, 45, 45, 45, 62, 62, 62, 62, 36, 36, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 36, 36, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 36, 1, 1, 1, 1] 62
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037791 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 19, 36, 36, 19, 28, 36, 36, 36, 36, 19, 19, 19, 19, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 36, 36, 36, 36] 62
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037791 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037791/1 /scratch/stefan/7769618/working/building/REAL300000037791 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/935
`/scratch/stefan/7769618/working/3D/935' -> `1.mol2'
Preparing input files

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

`REAL300000037791.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037791/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037791 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 17, 19, 19, 19, 19, 22, 22, 22, 30, 30, 30, 30, 19, 19, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 17, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 19, 1, 1, 1, 1] 30
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037791 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 10, 19, 19, 16, 19, 19, 19, 19, 19, 10, 10, 10, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 19, 19, 19, 19] 30
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 77
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037791 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037791
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037791/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037791/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037791
Building REAL300000037792
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037792'
/scratch/stefan/7769618/working/building/REAL300000037792 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037792

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037792/0 /scratch/stefan/7769618/working/building/REAL300000037792 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/936
`/scratch/stefan/7769618/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1)

`REAL300000037792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037792 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 130, 106, 130, 130, 106, 106, 106, 65, 65, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 9, 9, 1, 1, 1, 106] 201
rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 602
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037792 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 27, 106, 106, 106, 106, 106, 106, 106, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 27, 27, 106, 106, 106, 1] 201
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037792 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037792/1 /scratch/stefan/7769618/working/building/REAL300000037792 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/937
`/scratch/stefan/7769618/working/3D/937' -> `1.mol2'
Preparing input files

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

`REAL300000037792.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037792/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037792 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 26, 17, 26, 26, 17, 17, 17, 16, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 17, 16, 6, 1, 1, 1, 17] 40
rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037792 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 4, 11, 17, 17, 17, 1] 40
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037792 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037792
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037792/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037792/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037792
Building REAL300000037793
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037793'
/scratch/stefan/7769618/working/building/REAL300000037793 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037793

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037793/0 /scratch/stefan/7769618/working/building/REAL300000037793 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/938
`/scratch/stefan/7769618/working/3D/938' -> `0.mol2'
Preparing input files

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

`REAL300000037793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037793 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 18, 26, 26, 26, 26, 40, 40, 40, 52, 52, 52, 52, 26, 26, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 18, 26, 26, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 26, 1, 1, 1, 1] 52
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 197
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037793 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 14, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 26, 26, 26, 26] 52
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 70
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037793 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037793/1 /scratch/stefan/7769618/working/building/REAL300000037793 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/939
`/scratch/stefan/7769618/working/3D/939' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=CC=C1C(=O)[O-])

`REAL300000037793.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037793/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037793 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 17, 17, 32, 32, 32, 32, 38, 38, 38, 65, 65, 65, 65, 32, 32, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 32, 32, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 32, 1, 1, 1, 1] 65
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037793 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 25, 32, 32, 32, 32, 32, 32, 32, 32, 25, 25, 25, 25, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 32, 32, 32, 32] 65
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037793 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037793
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037793/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037793/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037793
Building REAL300000037794
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037794'
/scratch/stefan/7769618/working/building/REAL300000037794 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037794

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037794/0 /scratch/stefan/7769618/working/building/REAL300000037794 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/940
`/scratch/stefan/7769618/working/3D/940' -> `0.mol2'
Preparing input files

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

`REAL300000037794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037794 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 18, 28, 28, 28, 28, 41, 41, 41, 52, 52, 52, 52, 28, 28, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 18, 28, 28, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 28, 1, 1, 1, 1] 52
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 188
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037794 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 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]
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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 14, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 28, 28, 28, 28] 52
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 74
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037794 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037794/1 /scratch/stefan/7769618/working/building/REAL300000037794 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/941
`/scratch/stefan/7769618/working/3D/941' -> `1.mol2'
Preparing input files

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

`REAL300000037794.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037794/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037794 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 34, 34, 57, 57, 57, 57, 70, 70, 70, 108, 108, 108, 108, 57, 57, 1, 1, 1, 1, 1, 1, 2, 2, 1, 8, 8, 8, 8, 57, 57, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 57, 1, 1, 1, 1] 108
rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 334
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037794 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 19, 57, 57, 57, 57, 57, 57, 57, 57, 19, 19, 19, 19, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 57, 57, 57, 57] 108
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037794 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037794
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037794/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037794/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037794
Building REAL300000037795
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037795'
/scratch/stefan/7769618/working/building/REAL300000037795 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037795

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037795/0 /scratch/stefan/7769618/working/building/REAL300000037795 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/942
`/scratch/stefan/7769618/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1)

`REAL300000037795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037795 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 8, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 8, 13, 13, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 5, 5, 3, 3, 1, 8, 8, 5] 29
rigid atoms, others: [40, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43])
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: REAL300000037795 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 20, 21, 21, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 4, 5, 20, 20, 1] 29
rigid atoms, others: [43, 36, 5, 8, 9, 10, 11, 12, 13, 14, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037795 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037795
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037795/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037795
Building REAL300000037796
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037796'
/scratch/stefan/7769618/working/building/REAL300000037796 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037796

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037796/0 /scratch/stefan/7769618/working/building/REAL300000037796 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/943
`/scratch/stefan/7769618/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037796 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 14, 25, 25, 14, 14, 14, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 12, 6, 1, 1, 14] 35
rigid atoms, others: [39, 40, 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, 41])
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: REAL300000037796 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 14, 14, 14, 14, 14, 14, 14, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 11, 14, 14, 1] 35
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037796 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037796/1 /scratch/stefan/7769618/working/building/REAL300000037796 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/944
`/scratch/stefan/7769618/working/3D/944' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037796.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037796/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037796 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 124, 107, 124, 124, 107, 107, 107, 64, 63, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 8, 8, 1, 1, 107] 201
rigid atoms, others: [39, 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, 41])
total number of confs: 586
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037796 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 27, 106, 106, 106, 107, 105, 106, 106, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 27, 27, 106, 106, 1] 201
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037796 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037796
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037796/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037796/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037796
Building REAL300000037797
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037797'
/scratch/stefan/7769618/working/building/REAL300000037797 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037797

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037797/0 /scratch/stefan/7769618/working/building/REAL300000037797 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/945
`/scratch/stefan/7769618/working/3D/945' -> `0.mol2'
Preparing input files

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

`REAL300000037797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037797 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 18, 13, 18, 18, 13, 13, 13, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 7, 3, 1, 1, 2, 1, 13] 54
rigid atoms, others: [41, 42, 44, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 45])
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: REAL300000037797 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 4, 11, 13, 13, 26, 13, 1] 54
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037797 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037797/1 /scratch/stefan/7769618/working/building/REAL300000037797 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/946
`/scratch/stefan/7769618/working/3D/946' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1)

`REAL300000037797.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037797/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037797 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
258  conformations in input
total number of sets (complete confs): 258
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 129, 129, 78, 61, 78, 78, 61, 61, 61, 42, 42, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 61, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 61, 61, 7, 7, 1, 1, 2, 1, 61] 258
rigid atoms, others: [41, 42, 44, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 45])
total number of confs: 413
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037797 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
258  conformations in input
total number of sets (complete confs): 258
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 16, 61, 61, 61, 61, 61, 61, 62, 62, 61, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 16, 16, 61, 61, 122, 61, 1] 258
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037797 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037797
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037797/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037797/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037797
Building REAL300000037798
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037798'
/scratch/stefan/7769618/working/building/REAL300000037798 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037798

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037798/0 /scratch/stefan/7769618/working/building/REAL300000037798 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/947
`/scratch/stefan/7769618/working/3D/947' -> `0.mol2'
Preparing input files

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

`REAL300000037798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037798 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 66, 66, 96, 96, 96, 96, 113, 113, 113, 172, 172, 172, 172, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 96, 96, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 96, 1, 1] 172
rigid atoms, others: [1, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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])
total number of confs: 494
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037798 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [33, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 33, 96, 96, 96, 96, 96, 96, 96, 33, 33, 33, 33, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 96, 96] 172
rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 16, 17, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037798 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037798
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037798/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037798
Building REAL300000037799
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037799'
/scratch/stefan/7769618/working/building/REAL300000037799 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037799

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037799/0 /scratch/stefan/7769618/working/building/REAL300000037799 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/948
`/scratch/stefan/7769618/working/3D/948' -> `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=C(S(=O)(=O)NC(C)(C)C)C=N2)N1)

`REAL300000037799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037799 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 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: [86, 86, 86, 86, 100, 100, 86, 22, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 86, 86, 86, 86, 86, 22, 22, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 86] 201
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
total number of confs: 228
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037799 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 58, 58, 86, 86, 86, 86, 123, 123, 123, 201, 201, 201, 201, 86, 86, 1, 2, 2, 2, 1, 9, 9, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037799 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037799/1 /scratch/stefan/7769618/working/building/REAL300000037799 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/949
`/scratch/stefan/7769618/working/3D/949' -> `1.mol2'
Preparing input files

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

`REAL300000037799.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037799/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037799 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 10, 10, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 12, 12, 12, 12, 12, 10, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 12] 30
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
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: REAL300000037799 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 8, 12, 12, 12, 12, 20, 20, 20, 30, 30, 30, 30, 12, 12, 1, 2, 2, 2, 1, 4, 8, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 1] 30
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037799 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037799
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037799/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037799/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037799
Building REAL300000037800
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037800'
/scratch/stefan/7769618/working/building/REAL300000037800 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037800

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037800/0 /scratch/stefan/7769618/working/building/REAL300000037800 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/950
`/scratch/stefan/7769618/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1)

`REAL300000037800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037800 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 38, 62, 62, 38, 38, 38, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 38, 38, 1, 1, 1, 1, 1, 1, 38] 104
rigid atoms, others: [35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41])
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: REAL300000037800 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 51, 51, 38, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 38, 38, 38, 38, 38, 38, 1] 104
rigid atoms, others: [33, 34, 5, 8, 9, 10, 11, 12, 21, 22, 41] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037800 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037800
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037800/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037800
Building REAL300000037801
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037801'
/scratch/stefan/7769618/working/building/REAL300000037801 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037801

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037801/0 /scratch/stefan/7769618/working/building/REAL300000037801 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/951
`/scratch/stefan/7769618/working/3D/951' -> `0.mol2'
Preparing input files

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

`REAL300000037801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037801 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 14, 20, 20, 14, 14, 14, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 8, 3, 1, 1, 1, 1, 14] 28
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: 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: REAL300000037801 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 11, 14, 14, 14, 14, 1] 28
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037801 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037801/1 /scratch/stefan/7769618/working/building/REAL300000037801 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/952
`/scratch/stefan/7769618/working/3D/952' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1)

`REAL300000037801.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037801/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037801 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 122, 90, 122, 122, 90, 90, 90, 61, 61, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 8, 8, 1, 1, 1, 1, 90] 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: 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: REAL300000037801 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 4, 23, 90, 90, 90, 90, 90, 91, 91, 90, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 23, 23, 90, 90, 90, 90, 1] 201
rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037801 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037801
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037801/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037801/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037801
Building REAL300000037802
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037802'
/scratch/stefan/7769618/working/building/REAL300000037802 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037802

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037802/0 /scratch/stefan/7769618/working/building/REAL300000037802 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/953
`/scratch/stefan/7769618/working/3D/953' -> `0.mol2'
Preparing input files

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

`REAL300000037802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037802 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 21, 26, 26, 26, 26, 41, 41, 41, 56, 56, 56, 56, 26, 26, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 10, 21, 26, 26, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 26, 1, 1] 56
rigid atoms, others: [1, 43, 44, 18, 19, 20, 21, 22, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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: REAL300000037802 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 13, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 26, 26] 56
rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 16, 17, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 72
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037802 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037802
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037802/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037802
Building REAL300000037803
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037803'
/scratch/stefan/7769618/working/building/REAL300000037803 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037803

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037803/0 /scratch/stefan/7769618/working/building/REAL300000037803 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/954
`/scratch/stefan/7769618/working/3D/954' -> `0.mol2'
Preparing input files

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

`REAL300000037803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037803 none CC(CCCCCCC(=O)[O-])N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 6, 23, 49, 51, 57, 86, 90, 141, 154, 154, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 23, 23, 23, 23, 49, 49, 51, 51, 57, 57, 86, 86, 90, 90, 141, 141, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201
rigid atoms, others: [44, 43, 12, 13, 14, 15, 16, 17, 55, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 745
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037803 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037803
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037803/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037803
Building REAL300000037804
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037804'
/scratch/stefan/7769618/working/building/REAL300000037804 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037804

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037804/0 /scratch/stefan/7769618/working/building/REAL300000037804 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/955
`/scratch/stefan/7769618/working/3D/955' -> `0.mol2'
Preparing input files

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

`REAL300000037804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037804 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7, 15, 15, 15, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 7, 7, 7, 6, 7, 15, 15, 7, 7, 7, 7, 7, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 32
rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 50, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 49])
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: REAL300000037804 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 12, 12, 12, 22, 23, 23, 23, 7, 7, 2, 2, 2, 1, 1, 6, 6, 1, 1, 1, 1, 1, 7, 7, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7] 32
rigid atoms, others: [0, 1, 2, 3, 36, 33, 7, 8, 9, 10, 34, 35, 29, 30, 37] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 116
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037804 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037804
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037804/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037804
Building REAL300000037805
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037805'
/scratch/stefan/7769618/working/building/REAL300000037805 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037805

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037805/0 /scratch/stefan/7769618/working/building/REAL300000037805 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/956
`/scratch/stefan/7769618/working/3D/956' -> `0.mol2'
Preparing input files

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

`REAL300000037805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037805 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 49, 49, 75, 75, 75, 75, 83, 83, 83, 133, 133, 133, 133, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 75, 75, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 75, 1, 1] 133
rigid atoms, others: [1, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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])
total number of confs: 384
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037805 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 21, 75, 75, 75, 75, 75, 75, 75, 21, 21, 21, 21, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 75, 75] 133
rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 16, 17, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037805 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037805/1 /scratch/stefan/7769618/working/building/REAL300000037805 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/957
`/scratch/stefan/7769618/working/3D/957' -> `1.mol2'
Preparing input files

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

`REAL300000037805.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037805/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037805 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 20, 24, 24, 24, 24, 41, 41, 41, 64, 64, 64, 64, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 24, 24, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 24, 1, 1] 64
rigid atoms, others: [1, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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])
total number of confs: 253
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037805 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 14, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 24, 24] 64
rigid atoms, others: [3, 4, 5, 6, 7, 8, 42, 16, 17, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 64
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037805 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037805
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037805/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037805/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037805
Building REAL300000037806
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037806'
/scratch/stefan/7769618/working/building/REAL300000037806 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037806

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037806/0 /scratch/stefan/7769618/working/building/REAL300000037806 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/958
`/scratch/stefan/7769618/working/3D/958' -> `0.mol2'
Preparing input files

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

`REAL300000037806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037806 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [25, 25, 25, 25, 25, 32, 32, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 66
rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 50, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 49])
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: REAL300000037806 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 38, 38, 38, 66, 66, 66, 66, 25, 25, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 25] 66
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 34, 37, 35, 32, 36, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037806 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037806
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037806/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037806
Building REAL300000037807
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037807'
/scratch/stefan/7769618/working/building/REAL300000037807 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037807

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037807/0 /scratch/stefan/7769618/working/building/REAL300000037807 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/959
`/scratch/stefan/7769618/working/3D/959' -> `0.mol2'
Preparing input files

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

`REAL300000037807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037807 none CC1CC(N=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 20, 20, 20, 20, 20] 49
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 45, 18, 19] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50])
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: REAL300000037807 none CC1CC(N=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 20, 20, 20, 20, 28, 28, 28, 49, 49, 49, 49, 20, 20, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 20, 1, 1, 1, 1, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 32, 46, 47, 48, 49, 50, 20, 21, 22, 23, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037807 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037807
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037807/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037807
Building REAL300000037808
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037808'
/scratch/stefan/7769618/working/building/REAL300000037808 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037808

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037808/0 /scratch/stefan/7769618/working/building/REAL300000037808 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/960
`/scratch/stefan/7769618/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1)

`REAL300000037808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037808 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 136, 106, 136, 136, 106, 106, 106, 60, 60, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 8, 8, 1, 1, 1, 106] 201
rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 616
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037808 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 29, 106, 106, 106, 106, 107, 107, 106, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 29, 29, 106, 106, 106, 1] 201
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037808 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037808/1 /scratch/stefan/7769618/working/building/REAL300000037808 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/961
`/scratch/stefan/7769618/working/3D/961' -> `1.mol2'
Preparing input files

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

`REAL300000037808.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037808/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037808 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 18, 11, 18, 18, 11, 11, 11, 10, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 10, 5, 1, 1, 1, 11] 28
rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037808 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 9, 9, 11, 11, 11, 11, 11, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 9, 11, 11, 11, 1] 28
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037808 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037808
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037808/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037808/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037808
Building REAL300000037809
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037809'
/scratch/stefan/7769618/working/building/REAL300000037809 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037809

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037809/0 /scratch/stefan/7769618/working/building/REAL300000037809 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/962
`/scratch/stefan/7769618/working/3D/962' -> `0.mol2'
Preparing input files

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

`REAL300000037809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037809 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [17, 5, 17, 19, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 17, 17, 17, 17, 19, 19, 20, 20, 20, 20, 20, 20, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 40
rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 50, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 49])
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: REAL300000037809 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 4, 1, 1, 1, 2, 2, 1, 1, 1, 5, 14, 14, 20, 20, 20, 20, 29, 29, 29, 40, 40, 40, 40, 20, 20, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 20, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20] 40
rigid atoms, others: [32, 33, 2, 3, 4, 37, 7, 8, 9, 34, 35, 36] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037809 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037809
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037809/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037809
Building REAL300000037810
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037810'
/scratch/stefan/7769618/working/building/REAL300000037810 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037810

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037810/0 /scratch/stefan/7769618/working/building/REAL300000037810 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/963
`/scratch/stefan/7769618/working/3D/963' -> `0.mol2'
Preparing input files

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

`REAL300000037810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037810 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 15, 15, 15, 15, 11, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 25
rigid atoms, others: [32, 33, 44, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037810 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 1, 1, 4, 4, 11, 15, 15, 15, 15, 22, 22, 22, 25, 25, 25, 25, 15, 15, 2, 2, 2, 1, 4, 11, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 29] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037810 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037810/1 /scratch/stefan/7769618/working/building/REAL300000037810 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/964
`/scratch/stefan/7769618/working/3D/964' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)

`REAL300000037810.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037810/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037810 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 43, 43, 43, 43, 43, 46, 46, 23, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 44, 44, 44, 43, 23, 23, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 101
rigid atoms, others: [32, 33, 44, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037810 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 3, 1, 1, 5, 33, 34, 44, 44, 44, 44, 66, 66, 66, 101, 101, 101, 101, 44, 44, 2, 2, 2, 1, 5, 5, 44, 44, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 44] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 29] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037810 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037810
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037810/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037810/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037810
Building REAL300000037811
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037811'
/scratch/stefan/7769618/working/building/REAL300000037811 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037811

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037811/0 /scratch/stefan/7769618/working/building/REAL300000037811 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/965
`/scratch/stefan/7769618/working/3D/965' -> `0.mol2'
Preparing input files

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

`REAL300000037811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037811 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 27, 43, 43, 27, 27, 27, 21, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 27, 27, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 27, 27, 21, 7, 1, 1, 1, 27] 61
rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44])
total number of confs: 241
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037811 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 11, 27, 27, 27, 1] 61
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 44, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037811 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037811/1 /scratch/stefan/7769618/working/building/REAL300000037811 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/966
`/scratch/stefan/7769618/working/3D/966' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1)

`REAL300000037811.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037811/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037811 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 115, 75, 115, 115, 75, 75, 75, 46, 46, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 6, 6, 1, 1, 1, 75] 201
rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44])
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: REAL300000037811 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 17, 75, 75, 75, 75, 87, 87, 75, 75, 75, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 17, 17, 75, 75, 75, 1] 201
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 44, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037811 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037811
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037811/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037811/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037811
Building REAL300000037812
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037812'
/scratch/stefan/7769618/working/building/REAL300000037812 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037812

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037812/0 /scratch/stefan/7769618/working/building/REAL300000037812 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/967
`/scratch/stefan/7769618/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037812 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 148, 148, 148, 94, 148, 148, 94, 94, 94, 70, 70, 9, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 1, 94, 94, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 94, 94, 9, 9, 1, 1, 6, 6, 94] 201
rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 499
number of broken/clashed sets: 97
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037812 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 19, 94, 94, 94, 94, 147, 147, 155, 155, 94, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 19, 19, 94, 94, 147, 147, 1] 201
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 379
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037812 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037812/1 /scratch/stefan/7769618/working/building/REAL300000037812 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/968
`/scratch/stefan/7769618/working/3D/968' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037812.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037812/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037812 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [127, 113, 127, 127, 67, 40, 67, 67, 40, 40, 40, 24, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 1, 40, 40, 127, 127, 127, 127, 127, 127, 127, 127, 127, 113, 40, 40, 24, 6, 1, 1, 11, 11, 40] 201
rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 592
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037812 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 20, 20, 40, 40, 40, 40, 104, 104, 121, 121, 40, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 20, 40, 40, 104, 104, 1] 201
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 335
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037812 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037812
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037812/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037812/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037812
Building REAL300000037813
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037813'
/scratch/stefan/7769618/working/building/REAL300000037813 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037813

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037813/0 /scratch/stefan/7769618/working/building/REAL300000037813 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/969
`/scratch/stefan/7769618/working/3D/969' -> `0.mol2'
Preparing input files

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

`REAL300000037813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037813 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 23, 33, 33, 33, 33, 45, 45, 45, 60, 60, 60, 60, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 23, 33, 33, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 33, 1, 1, 1] 60
rigid atoms, others: [1, 44, 45, 46, 18, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 208
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: REAL300000037813 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 14, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 33, 33, 33] 60
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 81
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037813 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037813/1 /scratch/stefan/7769618/working/building/REAL300000037813 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/970
`/scratch/stefan/7769618/working/3D/970' -> `1.mol2'
Preparing input files

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

`REAL300000037813.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037813/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037813 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 39, 39, 54, 54, 54, 54, 77, 77, 77, 122, 122, 122, 122, 54, 54, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 54, 54, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 54, 1, 1, 1] 122
rigid atoms, others: [1, 44, 45, 46, 18, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 415
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037813 none CC(N=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 24, 54, 54, 54, 54, 54, 54, 54, 54, 24, 24, 24, 24, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 54, 54, 54] 122
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037813 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037813
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037813/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037813/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037813
Building REAL300000037814
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037814'
/scratch/stefan/7769618/working/building/REAL300000037814 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037814

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037814/0 /scratch/stefan/7769618/working/building/REAL300000037814 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/971
`/scratch/stefan/7769618/working/3D/971' -> `0.mol2'
Preparing input files

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

`REAL300000037814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037814 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 17, 27, 27, 17, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 17, 7, 1, 1, 1, 17] 43
rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43])
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: REAL300000037814 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 10, 17, 17, 17, 1] 43
rigid atoms, others: [43, 36, 5, 8, 9, 10, 11, 12, 24, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037814 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037814
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037814/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037814
Building REAL300000037815
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037815'
/scratch/stefan/7769618/working/building/REAL300000037815 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037815

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037815/0 /scratch/stefan/7769618/working/building/REAL300000037815 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/972
`/scratch/stefan/7769618/working/3D/972' -> `0.mol2'
Preparing input files

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

`REAL300000037815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037815 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 34, 22, 34, 34, 22, 22, 22, 17, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 22, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 17, 6, 1, 1, 2, 1, 22] 98
rigid atoms, others: [41, 42, 44, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 45])
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: REAL300000037815 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 11, 22, 22, 44, 22, 1] 98
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037815 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037815/1 /scratch/stefan/7769618/working/building/REAL300000037815 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/973
`/scratch/stefan/7769618/working/3D/973' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1)

`REAL300000037815.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037815/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037815 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 125, 82, 125, 125, 82, 82, 82, 47, 47, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 8, 8, 1, 1, 2, 1, 82] 402
rigid atoms, others: [41, 42, 44, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 45])
total number of confs: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037815 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 17, 82, 82, 82, 82, 99, 99, 82, 82, 82, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 17, 17, 82, 82, 164, 82, 1] 402
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 45, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 397
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037815 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037815
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037815/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037815/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037815
Building REAL300000037816
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037816'
/scratch/stefan/7769618/working/building/REAL300000037816 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037816

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037816/0 /scratch/stefan/7769618/working/building/REAL300000037816 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/974
`/scratch/stefan/7769618/working/3D/974' -> `0.mol2'
Preparing input files

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

`REAL300000037816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037816 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 12, 12, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 14] 43
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 46, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
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: REAL300000037816 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 25, 25, 25, 43, 43, 43, 43, 14, 14, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 4, 8, 14, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037816 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037816/1 /scratch/stefan/7769618/working/building/REAL300000037816 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/975
`/scratch/stefan/7769618/working/3D/975' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C=C1C(=O)[O-])

`REAL300000037816.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037816/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037816 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 76, 76, 76, 22, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 76, 76, 76, 106, 106, 77, 77, 77, 76, 76, 22, 22, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 76] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 46, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
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: REAL300000037816 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 56, 56, 76, 76, 76, 76, 112, 112, 112, 201, 201, 201, 201, 76, 76, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 76, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 702
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037816 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037816
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037816/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037816/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037816
Building REAL300000037817
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037817'
/scratch/stefan/7769618/working/building/REAL300000037817 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037817

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037817/0 /scratch/stefan/7769618/working/building/REAL300000037817 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/976
`/scratch/stefan/7769618/working/3D/976' -> `0.mol2'
Preparing input files

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

`REAL300000037817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037817 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 10, 10, 10, 10, 9, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 30
rigid atoms, others: [32, 33, 44, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037817 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 10, 10, 10, 10, 18, 18, 18, 30, 30, 30, 30, 10, 10, 2, 2, 2, 1, 4, 7, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037817 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037817/1 /scratch/stefan/7769618/working/building/REAL300000037817 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/977
`/scratch/stefan/7769618/working/3D/977' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1)

`REAL300000037817.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037817/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037817 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 97, 97, 97, 97, 29, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 97, 97, 97, 97, 29, 29, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 201
rigid atoms, others: [32, 33, 44, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
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: REAL300000037817 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 59, 59, 97, 97, 97, 97, 135, 135, 135, 201, 201, 201, 201, 97, 97, 2, 2, 2, 1, 8, 8, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 654
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037817 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037817
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037817/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037817/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037817
Building REAL300000037818
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037818'
/scratch/stefan/7769618/working/building/REAL300000037818 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037818

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037818/0 /scratch/stefan/7769618/working/building/REAL300000037818 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/978
`/scratch/stefan/7769618/working/3D/978' -> `0.mol2'
Preparing input files

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

`REAL300000037818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037818 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 27, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 83, 83, 83, 83, 83, 27, 27, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 170
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300000037818 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 57, 57, 83, 83, 83, 83, 108, 108, 108, 170, 170, 170, 170, 83, 83, 2, 2, 2, 1, 1, 8, 8, 83, 83, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 83] 170
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30] set([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, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 536
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037818 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037818/1 /scratch/stefan/7769618/working/building/REAL300000037818 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/979
`/scratch/stefan/7769618/working/3D/979' -> `1.mol2'
Preparing input files

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

`REAL300000037818.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037818/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037818 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 11, 11, 11, 11, 11, 11, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 29
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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: REAL300000037818 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 9, 11, 11, 11, 11, 17, 17, 17, 29, 29, 29, 29, 11, 11, 2, 2, 2, 1, 1, 4, 9, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11] 29
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 29, 30] set([5, 6, 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, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037818 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037818
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037818/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037818/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037818
Building REAL300000037819
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037819'
/scratch/stefan/7769618/working/building/REAL300000037819 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037819

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037819/0 /scratch/stefan/7769618/working/building/REAL300000037819 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/980
`/scratch/stefan/7769618/working/3D/980' -> `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=C(S(=O)(=O)NC(C)(C)C)C=N2)O1)

`REAL300000037819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037819 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 12, 12, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 22, 22, 22, 22, 22, 12, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 50
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037819 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 16, 22, 22, 22, 22, 36, 36, 36, 50, 50, 50, 50, 22, 22, 1, 2, 2, 2, 1, 7, 16, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22] 50
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037819 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037819/1 /scratch/stefan/7769618/working/building/REAL300000037819 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/981
`/scratch/stefan/7769618/working/3D/981' -> `1.mol2'
Preparing input files

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

`REAL300000037819.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037819/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037819 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.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, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [80, 80, 80, 80, 91, 91, 80, 20, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 80, 81, 81, 81, 80, 20, 20, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 201
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037819 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.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, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 60, 60, 80, 80, 80, 80, 110, 110, 110, 201, 201, 201, 201, 80, 80, 1, 2, 2, 2, 1, 8, 8, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 681
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037819 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037819
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037819/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037819/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037819
Building REAL300000037820
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037820'
/scratch/stefan/7769618/working/building/REAL300000037820 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037820

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037820/0 /scratch/stefan/7769618/working/building/REAL300000037820 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/982
`/scratch/stefan/7769618/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037820 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 25, 16, 25, 25, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16, 16, 7, 1, 1, 16] 39
rigid atoms, others: [39, 40, 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, 41])
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: REAL300000037820 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 10, 10, 16, 16, 16, 16, 16, 16, 16, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 10, 16, 16, 1] 39
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037820 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037820/1 /scratch/stefan/7769618/working/building/REAL300000037820 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/983
`/scratch/stefan/7769618/working/3D/983' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037820.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037820/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037820 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 201, 133, 122, 133, 133, 122, 122, 122, 70, 69, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 8, 8, 1, 1, 122] 201
rigid atoms, others: [39, 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, 41])
total number of confs: 537
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037820 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 34, 121, 121, 121, 122, 122, 121, 121, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 34, 34, 121, 121, 1] 201
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037820 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037820
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037820/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037820/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037820
Building REAL300000037821
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037821'
/scratch/stefan/7769618/working/building/REAL300000037821 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037821

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037821/0 /scratch/stefan/7769618/working/building/REAL300000037821 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/984
`/scratch/stefan/7769618/working/3D/984' -> `0.mol2'
Preparing input files

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

`REAL300000037821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037821 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 10, 10, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 4, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 15] 27
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 46, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
total number of confs: 49
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037821 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 10, 15, 15, 15, 15, 22, 22, 22, 27, 27, 27, 27, 15, 15, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 5, 10, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 22, 23, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 110
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037821 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037821/1 /scratch/stefan/7769618/working/building/REAL300000037821 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/985
`/scratch/stefan/7769618/working/3D/985' -> `1.mol2'
Preparing input files

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

`REAL300000037821.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037821/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037821 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 25, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 61, 61, 63, 63, 61, 61, 61, 61, 61, 61, 25, 25, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 61] 153
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 46, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037821 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 37, 38, 61, 61, 61, 61, 94, 94, 94, 153, 153, 153, 153, 61, 61, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 6, 61, 61, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 61, 1] 153
rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 22, 23, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 546
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037821 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037821
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037821/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037821/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037821
Building REAL300000037822
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037822'
/scratch/stefan/7769618/working/building/REAL300000037822 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037822

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037822/0 /scratch/stefan/7769618/working/building/REAL300000037822 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/986
`/scratch/stefan/7769618/working/3D/986' -> `0.mol2'
Preparing input files

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

`REAL300000037822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037822 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 100, 100, 97, 22, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 97, 97, 97, 97, 97, 22, 22, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 97] 201
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
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: REAL300000037822 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 65, 65, 97, 97, 97, 97, 122, 122, 122, 201, 201, 201, 201, 97, 97, 1, 2, 2, 2, 1, 9, 9, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037822 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037822/1 /scratch/stefan/7769618/working/building/REAL300000037822 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/987
`/scratch/stefan/7769618/working/3D/987' -> `1.mol2'
Preparing input files

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

`REAL300000037822.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037822/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037822 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [24, 24, 24, 24, 24, 24, 24, 12, 12, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 1, 1, 24, 24, 24, 24, 24, 12, 4, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 24] 54
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037822 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 18, 24, 24, 24, 24, 38, 38, 38, 54, 54, 54, 54, 24, 24, 1, 2, 2, 2, 1, 7, 18, 24, 24, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 24, 1] 54
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037822 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037822
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037822/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037822/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037822
Building REAL300000037823
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037823'
/scratch/stefan/7769618/working/building/REAL300000037823 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037823

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037823/0 /scratch/stefan/7769618/working/building/REAL300000037823 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/988
`/scratch/stefan/7769618/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1)

`REAL300000037823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037823 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
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, 39, 28, 39, 39, 28, 28, 28, 23, 9, 9, 1, 1, 1, 1, 3, 3, 1, 1, 1, 28, 28, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 28, 28, 23, 9, 1, 1, 28] 56
rigid atoms, others: [39, 40, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41])
total number of confs: 209
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037823 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 8, 8, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 13, 13, 28, 28, 28, 28, 28, 28, 28, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 6, 13, 28, 28, 1] 56
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 77
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037823 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037823
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037823/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037823
Building REAL300000037824
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037824'
/scratch/stefan/7769618/working/building/REAL300000037824 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037824

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037824/0 /scratch/stefan/7769618/working/building/REAL300000037824 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/989
`/scratch/stefan/7769618/working/3D/989' -> `0.mol2'
Preparing input files

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

`REAL300000037824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037824 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 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
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, 21, 12, 21, 21, 12, 12, 12, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 10, 4, 1, 1, 12] 29
rigid atoms, others: [39, 40, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41])
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: REAL300000037824 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 11, 11, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 11, 12, 12, 1] 29
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 41, 23, 24] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037824 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037824
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037824/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037824
Building REAL300000037825
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037825'
/scratch/stefan/7769618/working/building/REAL300000037825 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037825

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037825/0 /scratch/stefan/7769618/working/building/REAL300000037825 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/990
`/scratch/stefan/7769618/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037825 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 106, 106, 75, 106, 106, 75, 75, 75, 60, 60, 9, 1, 1, 1, 1, 1, 1, 7, 9, 18, 14, 1, 75, 75, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 75, 75, 9, 9, 1, 1, 7, 7, 9, 9, 75] 201
rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 364
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037825 none CC(C)(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 17, 75, 75, 75, 75, 149, 161, 170, 168, 75, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 17, 17, 75, 75, 149, 149, 161, 161, 1] 201
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 47, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 606
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037825 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037825/1 /scratch/stefan/7769618/working/building/REAL300000037825 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/991
`/scratch/stefan/7769618/working/3D/991' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037825.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037825/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037825 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 62, 70, 70, 45, 25, 45, 45, 25, 25, 25, 17, 7, 7, 1, 1, 1, 1, 1, 1, 8, 16, 29, 21, 1, 25, 25, 70, 70, 70, 70, 70, 70, 70, 70, 70, 62, 25, 25, 17, 7, 1, 1, 8, 8, 16, 16, 25] 201
rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 392
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037825 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 15, 15, 25, 25, 25, 25, 81, 105, 119, 114, 25, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 15, 25, 25, 81, 81, 105, 105, 1] 201
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 47, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037825 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037825
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037825/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037825/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037825
Building REAL300000037826
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037826'
/scratch/stefan/7769618/working/building/REAL300000037826 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037826

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037826/0 /scratch/stefan/7769618/working/building/REAL300000037826 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/992
`/scratch/stefan/7769618/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1)

`REAL300000037826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037826 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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, 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, 22, 15, 22, 22, 15, 15, 15, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 12, 5, 1, 1, 1, 15] 33
rigid atoms, others: [41, 42, 43, 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, 40, 44])
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: REAL300000037826 none CC(C)(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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, 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, 5, 7, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 4, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 4, 8, 15, 15, 15, 1] 33
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 44, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037826 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037826
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037826/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037826
Building REAL300000037827
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037827'
/scratch/stefan/7769618/working/building/REAL300000037827 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037827

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037827/0 /scratch/stefan/7769618/working/building/REAL300000037827 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/993
`/scratch/stefan/7769618/working/3D/993' -> `0.mol2'
Preparing input files

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

`REAL300000037827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037827 none CC1=NSC(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 9, 9, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 1, 1, 14, 14, 17, 17, 14, 14, 14, 9, 4, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 31
rigid atoms, others: [32, 43, 7, 8, 9, 10, 11, 12, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037827 none CC1=NSC(C=NNC2=CC=C(S(=O)(=O)NC(C)(C)C)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 14, 14, 14, 22, 22, 22, 31, 31, 31, 31, 14, 14, 1, 1, 3, 3, 2, 2, 2, 4, 9, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037827 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037827
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037827/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037827
Building REAL300000037828
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037828'
/scratch/stefan/7769618/working/building/REAL300000037828 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037828

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037828/0 /scratch/stefan/7769618/working/building/REAL300000037828 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/994
`/scratch/stefan/7769618/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C=C1)

`REAL300000037828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 68, 69, 48, 69, 69, 33, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 23, 23, 1, 1, 69, 69, 69, 69, 32, 33, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 69, 69] 201
rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 186, 56, 56, 23, 23, 23, 23, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 186, 186, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45])
total number of confs: 635
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 44, 79, 79, 79, 79, 106, 106, 106, 181, 201, 201, 201, 201, 79, 79, 1, 1, 1, 1, 7, 7, 79, 79, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037828 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037828/1 /scratch/stefan/7769618/working/building/REAL300000037828 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/995
`/scratch/stefan/7769618/working/3D/995' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C=C1)

`REAL300000037828.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037828/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [39, 19, 39, 19, 39, 39, 19, 19, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 1, 1, 39, 39, 39, 39, 19, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 39, 39] 113
rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 112, 113, 112, 113, 113, 112, 112, 49, 29, 29, 29, 29, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 29, 29, 113, 113, 113, 113, 112, 49, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 113, 113] 113
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45])
total number of confs: 257
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037828 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 26, 40, 40, 40, 40, 61, 61, 61, 106, 113, 113, 113, 113, 40, 40, 1, 1, 1, 1, 6, 26, 40, 40, 106, 113, 113, 113, 113, 113, 113, 113, 113, 113, 40, 1, 1] 113
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 404
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037828 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037828
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037828/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037828/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037828
Building REAL300000037829
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037829'
/scratch/stefan/7769618/working/building/REAL300000037829 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037829

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037829/0 /scratch/stefan/7769618/working/building/REAL300000037829 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/996
`/scratch/stefan/7769618/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [52, 43, 52, 43, 43, 43, 43, 43, 18, 18, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 28, 28, 1, 1, 43, 43, 43, 43, 18, 4, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1] 162
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 162, 162, 132, 132, 68, 28, 28, 28, 28, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 28, 28, 162, 162, 162, 162, 132, 68, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28] 162
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 360
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 43, 43, 43, 43, 68, 68, 68, 131, 162, 162, 162, 162, 43, 43, 1, 1, 1, 1, 6, 23, 43, 43, 131, 162, 162, 162, 162, 162, 162, 162, 162, 162, 43] 162
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: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037829 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037829/1 /scratch/stefan/7769618/working/building/REAL300000037829 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/997
`/scratch/stefan/7769618/working/3D/997' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037829.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037829/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 60, 70, 60, 60, 60, 60, 60, 23, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 60, 60, 60, 60, 23, 23, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 135, 40, 40, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 135, 135, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 562
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037829 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 39, 40, 60, 60, 60, 60, 90, 90, 90, 169, 201, 201, 201, 201, 60, 60, 1, 1, 1, 1, 6, 6, 60, 60, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60] 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, 42, 43, 44, 45])
total number of confs: 705
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037829 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037829
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037829/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037829/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037829
Building REAL300000037830
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037830'
/scratch/stefan/7769618/working/building/REAL300000037830 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037830

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037830/0 /scratch/stefan/7769618/working/building/REAL300000037830 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/998
`/scratch/stefan/7769618/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1)

`REAL300000037830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 18, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 72, 72, 72, 18, 18, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 72] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 101, 34, 34, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 101, 101, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43])
total number of confs: 511
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 56, 72, 72, 72, 72, 94, 94, 94, 173, 201, 201, 201, 201, 72, 72, 1, 1, 1, 8, 8, 72, 72, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 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: 645
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037830 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037830/1 /scratch/stefan/7769618/working/building/REAL300000037830 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/999
`/scratch/stefan/7769618/working/3D/999' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1)

`REAL300000037830.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037830/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 19, 19, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 30, 30, 30, 1, 1, 65, 65, 65, 19, 4, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 65] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 163, 163, 64, 30, 30, 30, 30, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 163, 65, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43])
total number of confs: 420
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037830 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 65, 65, 65, 65, 100, 100, 100, 187, 201, 201, 201, 201, 65, 65, 1, 1, 1, 9, 41, 65, 65, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 25, 26, 27] set([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: 706
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037830 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037830
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037830/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037830/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037830
Building REAL300000037831
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037831'
/scratch/stefan/7769618/working/building/REAL300000037831 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037831

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037831/0 /scratch/stefan/7769618/working/building/REAL300000037831 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1000
`/scratch/stefan/7769618/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N=N1)

`REAL300000037831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037831 none O=C([O-])CN1C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 48, 48, 48, 13, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 1, 1, 48, 48, 87, 87, 48, 13, 13, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 351
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037831 none O=C([O-])CN1C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 164, 164, 164, 60, 22, 22, 15, 15, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 15, 15, 164, 164, 201, 201, 164, 60, 60, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44])
total number of confs: 590
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037831 none O=C([O-])CN1C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 9, 46, 46, 48, 48, 48, 48, 64, 64, 64, 110, 164, 164, 164, 164, 48, 48, 1, 1, 4, 4, 1, 9, 9, 48, 48, 110, 164, 164, 164, 164, 164, 164, 164, 164, 164, 48] 201
rigid atoms, others: [3, 4, 5, 6, 7, 25, 26, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 549
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037831 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037831
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037831/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037831
Building REAL300000037832
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037832'
/scratch/stefan/7769618/working/building/REAL300000037832 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037832

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037832/0 /scratch/stefan/7769618/working/building/REAL300000037832 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1001
`/scratch/stefan/7769618/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 62, 62, 62, 62, 20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 27, 27, 1, 1, 62, 62, 20, 4, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 62] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 41, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 160
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 159, 159, 63, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 159, 63, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 420
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 37, 62, 62, 62, 62, 92, 92, 92, 191, 201, 201, 201, 201, 62, 62, 1, 1, 11, 37, 62, 62, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 668
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037832 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037832/1 /scratch/stefan/7769618/working/building/REAL300000037832 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1002
`/scratch/stefan/7769618/working/3D/1002' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037832.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037832/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 13, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 1, 1, 64, 64, 13, 13, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 64] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 41, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 24, 24, 16, 16, 16, 16, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 82, 82, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 457
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037832 none O=C([O-])C1=CSC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', '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, 14, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 56, 56, 64, 64, 64, 64, 91, 91, 91, 181, 201, 201, 201, 201, 64, 64, 1, 1, 9, 9, 64, 64, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 661
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037832 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037832
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037832/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037832/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037832
Building REAL300000037833
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037833'
/scratch/stefan/7769618/working/building/REAL300000037833 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037833

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037833/0 /scratch/stefan/7769618/working/building/REAL300000037833 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1003
`/scratch/stefan/7769618/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)C1=CC=C(C(=O)[O-])O1)

`REAL300000037833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037833 none CC(N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 42, 20, 20, 20, 20, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 20, 20, 110, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45])
total number of confs: 510
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037833 none CC(N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 49, 87, 87, 87, 87, 113, 113, 113, 198, 201, 201, 201, 201, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 87, 87, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 1, 1] 201
rigid atoms, others: [1, 44, 45, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 620
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037833 none CC(N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 1, 1, 23, 87, 87, 87, 87, 87, 87, 87, 23, 23, 23, 23, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 87, 87] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 43, 17, 18, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 214
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037833 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037833
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037833/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037833
Building REAL300000037834
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037834'
/scratch/stefan/7769618/working/building/REAL300000037834 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037834

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037834/0 /scratch/stefan/7769618/working/building/REAL300000037834 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1004
`/scratch/stefan/7769618/working/3D/1004' -> `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=C(S(=O)(=O)NC3CCCC3)C=N2)N1)

`REAL300000037834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 16, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 1, 1, 65, 65, 65, 65, 65, 16, 16, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 65] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 98, 22, 22, 14, 14, 14, 14, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 14, 14, 201, 201, 201, 201, 201, 98, 98, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 52, 52, 65, 65, 65, 65, 101, 101, 101, 188, 201, 201, 201, 201, 65, 65, 1, 2, 2, 2, 1, 9, 9, 65, 65, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 46, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 717
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037834 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037834/1 /scratch/stefan/7769618/working/building/REAL300000037834 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1005
`/scratch/stefan/7769618/working/3D/1005' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1)

`REAL300000037834.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037834/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 72, 72, 45, 20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 27, 27, 1, 1, 45, 45, 45, 45, 45, 20, 4, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 45] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 170, 170, 66, 27, 27, 27, 27, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 170, 66, 27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46])
total number of confs: 404
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037834 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 27, 45, 45, 45, 45, 74, 74, 74, 159, 201, 201, 201, 201, 45, 45, 1, 2, 2, 2, 1, 7, 26, 45, 45, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 45, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 46, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 701
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037834 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037834
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037834/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037834/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037834
Building REAL300000037835
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037835'
/scratch/stefan/7769618/working/building/REAL300000037835 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037835

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037835/0 /scratch/stefan/7769618/working/building/REAL300000037835 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1006
`/scratch/stefan/7769618/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C1)

`REAL300000037835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037835 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 40, 63, 40, 40, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 26, 26, 1, 1, 40, 40, 40, 40, 40, 1, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 40, 40] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 40, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037835 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 82, 82, 26, 26, 26, 26, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 201, 201, 201, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037835 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 40, 40, 40, 40, 64, 64, 64, 143, 201, 201, 201, 201, 40, 40, 1, 1, 1, 1, 1, 40, 40, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 40, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 659
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037835 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037835
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037835/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037835
Building REAL300000037836
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037836'
/scratch/stefan/7769618/working/building/REAL300000037836 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037836

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037836/0 /scratch/stefan/7769618/working/building/REAL300000037836 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1007
`/scratch/stefan/7769618/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 32, 32, 32, 1, 1, 68, 68, 68, 68, 22, 4, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 68] 201
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 174, 174, 70, 32, 32, 32, 32, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 201, 174, 70, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 201] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45])
total number of confs: 410
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 42, 68, 68, 68, 68, 97, 97, 97, 182, 201, 201, 201, 201, 68, 68, 1, 1, 1, 1, 9, 42, 68, 68, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 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: 693
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037836 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037836/1 /scratch/stefan/7769618/working/building/REAL300000037836 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1008
`/scratch/stefan/7769618/working/3D/1008' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037836.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037836/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 58, 58, 16, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 58, 58, 58, 58, 16, 16, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 58] 201
rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 96, 27, 27, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 96, 96, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 201] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45])
total number of confs: 487
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037836 none O=C([O-])C1=CC=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=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.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 48, 48, 58, 58, 58, 58, 91, 91, 91, 194, 201, 201, 201, 201, 58, 58, 1, 1, 1, 1, 8, 8, 58, 58, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 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: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037836 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037836
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037836/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037836/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037836
Building REAL300000037837
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037837'
/scratch/stefan/7769618/working/building/REAL300000037837 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037837

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037837/0 /scratch/stefan/7769618/working/building/REAL300000037837 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1009
`/scratch/stefan/7769618/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037837 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 59, 74, 74, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 25, 1, 1, 28, 28, 28, 26, 28, 59, 59, 28, 28, 28, 28, 28, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 201
rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 50])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037837 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 142, 142, 201, 201, 201, 142, 142, 61, 61, 25, 25, 25, 25, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 25, 25, 142, 142, 142, 137, 142, 201, 201, 142, 142, 142, 142, 142, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51])
total number of confs: 703
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037837 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 9, 1, 1, 1, 1, 9, 9, 28, 28, 28, 28, 47, 47, 47, 120, 142, 142, 142, 142, 28, 28, 2, 2, 2, 1, 1, 6, 6, 1, 1, 1, 1, 1, 28, 28, 120, 142, 142, 142, 142, 142, 142, 142, 142, 142, 28] 201
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 7, 8, 9, 10, 34, 35, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037837 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037837
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037837/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037837
Building REAL300000037838
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037838'
/scratch/stefan/7769618/working/building/REAL300000037838 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037838

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037838/0 /scratch/stefan/7769618/working/building/REAL300000037838 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1010
`/scratch/stefan/7769618/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037838 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 36, 36, 63, 63, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 28, 28, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1] 201
rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 50])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037838 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 106, 106, 28, 28, 28, 28, 15, 5, 15, 15, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28] 201
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51])
total number of confs: 492
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037838 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 1, 1, 1, 1, 6, 6, 36, 36, 36, 36, 56, 56, 56, 111, 201, 201, 201, 201, 36, 36, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 10, 7, 34, 35, 36, 37, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 658
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037838 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037838
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037838/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037838
Building REAL300000037839
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037839'
/scratch/stefan/7769618/working/building/REAL300000037839 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037839

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037839/0 /scratch/stefan/7769618/working/building/REAL300000037839 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1011
`/scratch/stefan/7769618/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)CCC1C(=O)[O-])

`REAL300000037839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037839 none CC1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 34, 34, 34, 34, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 73, 73, 73, 73, 73] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 46, 19, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51])
total number of confs: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037839 none CC1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 110, 110, 34, 34, 34, 34, 18, 6, 18, 18, 1, 1, 1, 1, 1, 1, 34, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 201, 201, 201, 201, 201] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037839 none CC1CC(N=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 73, 73, 73, 73, 113, 113, 113, 190, 201, 201, 201, 201, 73, 73, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 73, 73, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 48, 49, 50, 51, 21, 22, 23, 24, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037839 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037839
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037839/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037839
Building REAL300000037840
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037840'
/scratch/stefan/7769618/working/building/REAL300000037840 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037840

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037840/0 /scratch/stefan/7769618/working/building/REAL300000037840 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1012
`/scratch/stefan/7769618/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CN1)

`REAL300000037840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 70, 70, 70, 18, 18, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 70, 70] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 41, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 105, 29, 29, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 105, 105, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43])
total number of confs: 518
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 54, 54, 70, 70, 70, 70, 96, 96, 96, 170, 201, 201, 201, 201, 70, 70, 1, 1, 1, 8, 8, 70, 70, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037840 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037840/1 /scratch/stefan/7769618/working/building/REAL300000037840 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1013
`/scratch/stefan/7769618/working/3D/1013' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CN1)

`REAL300000037840.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037840/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 1, 1, 68, 68, 68, 22, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 68, 68] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 41, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 169, 169, 66, 29, 29, 29, 29, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 169, 66, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43])
total number of confs: 418
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037840 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 40, 68, 68, 68, 68, 103, 103, 103, 193, 201, 201, 201, 201, 68, 68, 1, 1, 1, 9, 40, 68, 68, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 691
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037840 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037840
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037840/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037840/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037840
Building REAL300000037841
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037841'
/scratch/stefan/7769618/working/building/REAL300000037841 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037841

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037841/0 /scratch/stefan/7769618/working/building/REAL300000037841 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1014
`/scratch/stefan/7769618/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037841 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [37, 8, 37, 45, 61, 61, 61, 61, 61, 61, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 31, 31, 31, 1, 1, 37, 37, 37, 37, 45, 45, 61, 61, 61, 61, 61, 61, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 189
rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 51, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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, 50])
total number of confs: 303
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037841 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [174, 102, 174, 177, 189, 189, 189, 189, 189, 189, 102, 31, 31, 31, 31, 18, 6, 18, 18, 1, 1, 1, 1, 1, 1, 31, 31, 174, 174, 174, 174, 177, 177, 189, 189, 189, 189, 189, 189, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 189
rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51])
total number of confs: 578
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037841 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 5, 1, 1, 1, 2, 2, 1, 1, 1, 6, 25, 25, 61, 61, 61, 61, 91, 91, 91, 163, 189, 189, 189, 189, 61, 61, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 61, 61, 163, 189, 189, 189, 189, 189, 189, 189, 189, 189, 61] 189
rigid atoms, others: [33, 2, 3, 4, 37, 38, 7, 8, 9, 34, 35, 36] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037841 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037841
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037841/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037841
Building REAL300000037842
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037842'
/scratch/stefan/7769618/working/building/REAL300000037842 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037842

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037842/0 /scratch/stefan/7769618/working/building/REAL300000037842 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1015
`/scratch/stefan/7769618/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 40, 40, 21, 21, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 30, 30, 30, 1, 1, 35, 35, 35, 35, 21, 7, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 166
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 166, 166, 166, 166, 166, 166, 166, 149, 149, 79, 30, 30, 30, 30, 18, 6, 18, 18, 1, 1, 1, 1, 1, 1, 30, 30, 166, 166, 166, 166, 149, 79, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 166
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 369
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 17, 35, 35, 35, 35, 58, 58, 58, 125, 164, 164, 164, 164, 35, 35, 2, 2, 2, 1, 4, 17, 35, 35, 125, 164, 164, 164, 164, 164, 164, 164, 164, 164, 35] 164
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 30] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037842 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037842/1 /scratch/stefan/7769618/working/building/REAL300000037842 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1016
`/scratch/stefan/7769618/working/3D/1016' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037842.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037842/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 58, 58, 27, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 1, 1, 58, 58, 58, 57, 27, 27, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 201
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 199
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 163, 44, 44, 20, 20, 20, 20, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 163, 163, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 610
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037842 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 39, 40, 58, 58, 58, 58, 94, 94, 94, 186, 201, 201, 201, 201, 58, 58, 2, 2, 2, 1, 5, 5, 58, 58, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 30] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 714
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037842 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037842
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037842/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037842/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037842
Building REAL300000037843
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037843'
/scratch/stefan/7769618/working/building/REAL300000037843 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037843

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037843/0 /scratch/stefan/7769618/working/building/REAL300000037843 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1017
`/scratch/stefan/7769618/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)C=N1)

`REAL300000037843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037843 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 83, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 27, 27, 1, 1, 83, 83, 83, 83, 22, 4, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 83] 194
rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037843 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 194, 194, 194, 108, 108, 48, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 27, 27, 194, 194, 194, 194, 108, 48, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 194] 194
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44])
total number of confs: 408
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037843 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 49, 83, 83, 83, 83, 122, 122, 122, 182, 194, 194, 194, 194, 83, 83, 1, 1, 1, 1, 10, 49, 83, 83, 182, 194, 194, 194, 194, 194, 194, 194, 194, 194, 83, 1] 194
rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 690
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037843 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037843
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037843/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037843
Building REAL300000037844
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037844'
/scratch/stefan/7769618/working/building/REAL300000037844 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037844

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037844/0 /scratch/stefan/7769618/working/building/REAL300000037844 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1018
`/scratch/stefan/7769618/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 31, 31, 31, 1, 1, 63, 63, 63, 63, 22, 4, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 201
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 68, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 164, 69, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 428
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 63, 63, 63, 63, 93, 93, 93, 188, 201, 201, 201, 201, 63, 63, 2, 2, 2, 1, 8, 36, 63, 63, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 678
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037844 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037844/1 /scratch/stefan/7769618/working/building/REAL300000037844 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1019
`/scratch/stefan/7769618/working/3D/1019' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037844.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037844/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 20, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 69, 69, 69, 69, 20, 20, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201
rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 103, 29, 29, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 103, 103, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 493
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037844 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 69, 69, 69, 69, 96, 96, 96, 190, 201, 201, 201, 201, 69, 69, 2, 2, 2, 1, 8, 8, 69, 69, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 656
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037844 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037844
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037844/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037844/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037844
Building REAL300000037845
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037845'
/scratch/stefan/7769618/working/building/REAL300000037845 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037845

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037845/0 /scratch/stefan/7769618/working/building/REAL300000037845 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1020
`/scratch/stefan/7769618/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 64, 21, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 1, 1, 64, 64, 64, 64, 64, 21, 21, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 201
rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 99, 32, 32, 16, 16, 16, 16, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 99, 99, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 8, 51, 51, 64, 64, 64, 64, 93, 93, 93, 192, 201, 201, 201, 201, 64, 64, 2, 2, 2, 1, 1, 8, 8, 64, 64, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([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, 42, 43, 44, 45, 46])
total number of confs: 665
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037845 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037845/1 /scratch/stefan/7769618/working/building/REAL300000037845 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1021
`/scratch/stefan/7769618/working/3D/1021' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1)

`REAL300000037845.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037845/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 63, 63, 63, 23, 23, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 31, 31, 31, 1, 1, 63, 63, 63, 63, 63, 23, 4, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 201
rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 164, 164, 70, 31, 31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 164, 71, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46])
total number of confs: 430
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037845 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC2CCCC2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 2, 2, 1, 1, 1, 9, 9, 37, 63, 63, 63, 63, 94, 94, 94, 187, 201, 201, 201, 201, 63, 63, 2, 2, 2, 1, 1, 9, 37, 63, 63, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63] 201
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 30, 31] set([5, 6, 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, 42, 43, 44, 45, 46])
total number of confs: 694
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037845 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037845
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037845/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037845/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037845
Building REAL300000037846
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037846'
/scratch/stefan/7769618/working/building/REAL300000037846 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037846

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037846/0 /scratch/stefan/7769618/working/building/REAL300000037846 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1022
`/scratch/stefan/7769618/working/3D/1022' -> `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=C(S(=O)(=O)NC3CCCC3)C=N2)O1)

`REAL300000037846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 71, 71, 52, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 31, 31, 31, 1, 1, 52, 52, 52, 52, 52, 16, 4, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 66, 31, 31, 31, 31, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 141, 66, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 435
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 30, 52, 52, 52, 52, 81, 81, 81, 167, 201, 201, 201, 201, 52, 52, 1, 2, 2, 2, 1, 8, 30, 52, 52, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 693
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037846 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037846/1 /scratch/stefan/7769618/working/building/REAL300000037846 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1023
`/scratch/stefan/7769618/working/3D/1023' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1)

`REAL300000037846.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037846/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.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, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 13, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 1, 1, 69, 69, 69, 69, 69, 13, 13, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.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, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 68, 27, 27, 15, 15, 15, 15, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201, 201, 68, 68, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45])
total number of confs: 429
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037846 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.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, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 58, 58, 69, 69, 69, 69, 97, 97, 97, 186, 201, 201, 201, 201, 69, 69, 1, 2, 2, 2, 1, 8, 8, 69, 69, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037846 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037846
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037846/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037846/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037846
Building REAL300000037847
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037847'
/scratch/stefan/7769618/working/building/REAL300000037847 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037847

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037847/0 /scratch/stefan/7769618/working/building/REAL300000037847 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1024
`/scratch/stefan/7769618/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', '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, 12, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 25, 1, 1, 80, 80, 22, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 80] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 41, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', '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, 12, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 155, 155, 62, 25, 25, 25, 25, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 25, 25, 201, 201, 155, 62, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 406
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=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.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.ar', 'N.ar', '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, 12, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 51, 80, 80, 80, 80, 123, 123, 123, 188, 201, 201, 201, 201, 80, 80, 1, 1, 11, 51, 80, 80, 188, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 727
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037847 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037847/1 /scratch/stefan/7769618/working/building/REAL300000037847 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1025
`/scratch/stefan/7769618/working/3D/1025' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037847.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037847/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', '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, 12, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 1, 1, 69, 69, 18, 18, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 69] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 41, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', '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, 12, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 99, 33, 33, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 99, 99, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 525
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037847 none O=C([O-])C1=COC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', '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, 12, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 55, 56, 69, 69, 69, 69, 94, 94, 94, 163, 201, 201, 201, 201, 69, 69, 1, 1, 8, 8, 69, 69, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037847 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037847
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037847/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037847/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037847
Building REAL300000037848
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037848'
/scratch/stefan/7769618/working/building/REAL300000037848 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037848

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037848/0 /scratch/stefan/7769618/working/building/REAL300000037848 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1026
`/scratch/stefan/7769618/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 15, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 1, 1, 66, 66, 66, 66, 66, 15, 15, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 66] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 26, 26, 16, 16, 16, 16, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 76, 76, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46])
total number of confs: 434
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 52, 52, 66, 66, 66, 66, 89, 89, 89, 185, 201, 201, 201, 201, 66, 66, 1, 2, 2, 2, 1, 8, 8, 66, 66, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 46, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 666
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037848 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037848/1 /scratch/stefan/7769618/working/building/REAL300000037848 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1027
`/scratch/stefan/7769618/working/3D/1027' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1)

`REAL300000037848.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037848/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 74, 74, 52, 20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 28, 28, 28, 1, 1, 52, 52, 52, 52, 52, 20, 4, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 52] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 149, 149, 63, 28, 28, 28, 28, 15, 5, 15, 15, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 201, 201, 201, 149, 63, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46])
total number of confs: 420
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037848 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 27, 52, 52, 52, 52, 79, 79, 79, 161, 201, 201, 201, 201, 52, 52, 1, 2, 2, 2, 1, 8, 27, 52, 52, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 46, 26, 30] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 694
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037848 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037848
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037848/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037848/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037848
Building REAL300000037849
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037849'
/scratch/stefan/7769618/working/building/REAL300000037849 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037849

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037849/0 /scratch/stefan/7769618/working/building/REAL300000037849 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1028
`/scratch/stefan/7769618/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)SC=C1)

`REAL300000037849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037849 none O=C([O-])C1=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [45, 36, 45, 36, 17, 17, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 32, 32, 32, 1, 1, 36, 36, 36, 17, 4, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 36, 36] 163
rigid atoms, others: [7, 8, 9, 10, 11, 12, 40, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037849 none O=C([O-])C1=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 133, 133, 71, 32, 32, 32, 32, 18, 6, 18, 18, 1, 1, 1, 1, 1, 1, 32, 32, 163, 163, 163, 133, 72, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 163, 163] 163
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42])
total number of confs: 384
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037849 none O=C([O-])C1=C(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 17, 36, 36, 36, 36, 60, 60, 60, 123, 163, 163, 163, 163, 36, 36, 1, 1, 1, 3, 17, 36, 36, 123, 163, 163, 163, 163, 163, 163, 163, 163, 163, 36, 1, 1] 163
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: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037849 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037849
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037849/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037849
Building REAL300000037850
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037850'
/scratch/stefan/7769618/working/building/REAL300000037850 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037850

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037850/0 /scratch/stefan/7769618/working/building/REAL300000037850 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1029
`/scratch/stefan/7769618/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CS1)

`REAL300000037850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037850 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 1, 1, 62, 62, 62, 22, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 62] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 41, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037850 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 162, 162, 67, 29, 29, 29, 29, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 162, 67, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42])
total number of confs: 417
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037850 none O=C([O-])C1=CC(C=NNC2=CC=C(S(=O)(=O)NC3CCCC3)C=N2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 7, 7, 6, 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, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 34, 62, 62, 62, 62, 95, 95, 95, 192, 201, 201, 201, 201, 62, 62, 1, 1, 1, 7, 34, 62, 62, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 42, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037850 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037850
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037850/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037850
Building REAL300000037851
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037851'
/scratch/stefan/7769618/working/building/REAL300000037851 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037851

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037851/0 /scratch/stefan/7769618/working/building/REAL300000037851 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1030
`/scratch/stefan/7769618/working/3D/1030' -> `0.mol2'
Preparing input files

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

`REAL300000037851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037851 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 37, 37, 23, 20, 23, 23, 13, 13, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 21, 23, 23, 13, 5, 1, 1, 1, 1, 22] 37
rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 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: REAL300000037851 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 23, 23, 17, 23, 23, 23, 23, 23, 1, 3, 3, 3, 1, 1, 1, 7, 17, 23, 23, 23, 23, 1] 37
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 2, 3, 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: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037851 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037851
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037851/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037851
Building REAL300000037852
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037852'
/scratch/stefan/7769618/working/building/REAL300000037852 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037852

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037852/0 /scratch/stefan/7769618/working/building/REAL300000037852 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1031
`/scratch/stefan/7769618/working/3D/1031' -> `0.mol2'
Preparing input files

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

`REAL300000037852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037852 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 35, 57, 57, 35, 10, 35, 35, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 54, 54, 35, 57, 57, 57, 10, 35, 35, 10, 4, 1, 1, 1, 1, 35, 35, 35] 201
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 409
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037852 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 35, 35, 13, 35, 35, 35, 95, 161, 161, 161, 1, 3, 3, 3, 1, 1, 1, 5, 13, 35, 35, 35, 35, 161, 161, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 40, 25, 29, 30, 31] set([0, 2, 3, 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: 535
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037852 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037852
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037852/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037852
Building REAL300000037853
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037853'
/scratch/stefan/7769618/working/building/REAL300000037853 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037853

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037853/0 /scratch/stefan/7769618/working/building/REAL300000037853 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1032
`/scratch/stefan/7769618/working/3D/1032' -> `0.mol2'
Preparing input files

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

`REAL300000037853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037853 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 36, 53, 53, 36, 12, 36, 36, 12, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 20, 32, 32, 1, 1, 36, 53, 53, 53, 12, 36, 36, 11, 5, 1, 1, 20, 20, 1, 1, 36] 201
rigid atoms, others: [34, 35, 38, 39, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40])
total number of confs: 317
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: REAL300000037853 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 5, 5, 21, 21, 34, 36, 21, 36, 88, 130, 131, 131, 36, 36, 1, 3, 3, 3, 1, 1, 1, 5, 21, 36, 36, 130, 130, 36, 36, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 40, 25, 29, 30, 31] set([0, 2, 3, 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: 408
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037853 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037853
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037853/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037853
Building REAL300000037854
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037854'
/scratch/stefan/7769618/working/building/REAL300000037854 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037854

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037854/0 /scratch/stefan/7769618/working/building/REAL300000037854 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1033
`/scratch/stefan/7769618/working/3D/1033' -> `0.mol2'
Preparing input files

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

`REAL300000037854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037854 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 7, 7, 7, 21, 21, 13, 21, 21, 37, 37, 37, 21, 1, 1, 1, 1, 1, 1, 5, 17, 21, 21, 1, 5, 5, 5, 7, 21, 21, 21, 37, 37, 37, 21, 1, 1, 1, 17, 17, 1] 201
rigid atoms, others: [1, 38, 39, 40, 43, 16, 17, 18, 19, 20, 21, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42])
total number of confs: 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: REAL300000037854 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.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', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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: [9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 21, 21, 21, 21, 21, 67, 120, 128, 128, 21, 9, 9, 9, 5, 1, 1, 1, 3, 3, 3, 1, 21, 21, 21, 120, 120, 21] 201
rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 15, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 421
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037854 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037854
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037854/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037854
Building REAL300000037855
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037855'
/scratch/stefan/7769618/working/building/REAL300000037855 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037855

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037855/0 /scratch/stefan/7769618/working/building/REAL300000037855 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1034
`/scratch/stefan/7769618/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])=C1)

`REAL300000037855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037855 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 41, 41, 25, 10, 25, 25, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 41, 41, 41, 10, 25, 25, 10, 6, 1, 1, 1, 1, 25] 41
rigid atoms, others: [32, 33, 34, 35, 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, 36])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037855 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 25, 25, 25, 25, 25, 25, 27, 27, 1, 3, 3, 3, 1, 1, 1, 7, 11, 25, 25, 25, 25, 1] 41
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 2, 3, 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: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037855 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037855
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037855/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037855
Building REAL300000037856
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037856'
/scratch/stefan/7769618/working/building/REAL300000037856 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037856

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037856/0 /scratch/stefan/7769618/working/building/REAL300000037856 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1035
`/scratch/stefan/7769618/working/3D/1035' -> `0.mol2'
Preparing input files

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

`REAL300000037856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037856 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 4, 4, 10, 10, 10, 25, 25, 10, 25, 25, 47, 47, 47, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 25, 25, 10, 47, 47, 47, 25, 1, 1, 1, 1] 47
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 210
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037856 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 25, 25, 11, 11, 25, 25, 25, 25, 11, 11, 11, 7, 1, 1, 1, 3, 3, 3, 1, 25, 25, 25, 25] 47
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 131
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037856 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037856
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037856/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037856
Building REAL300000037857
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037857'
/scratch/stefan/7769618/working/building/REAL300000037857 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037857

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037857/0 /scratch/stefan/7769618/working/building/REAL300000037857 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1036
`/scratch/stefan/7769618/working/3D/1036' -> `0.mol2'
Preparing input files

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

`REAL300000037857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037857 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
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: [6, 1, 6, 6, 16, 16, 16, 46, 46, 46, 46, 46, 74, 74, 74, 46, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 6, 6, 6, 16, 45, 46, 46, 74, 74, 74, 46, 1, 1, 3, 3, 1, 1] 116
rigid atoms, others: [1, 37, 38, 41, 42, 16, 17, 18, 19, 20, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 274
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037857 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
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: [21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 46, 46, 29, 46, 74, 76, 76, 46, 46, 21, 21, 21, 7, 1, 1, 1, 3, 3, 3, 1, 46, 46, 74, 74, 46, 46] 116
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 331
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037857 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037857
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037857/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037857
Building REAL300000037858
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037858'
/scratch/stefan/7769618/working/building/REAL300000037858 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037858

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037858/0 /scratch/stefan/7769618/working/building/REAL300000037858 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1037
`/scratch/stefan/7769618/working/3D/1037' -> `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=CC(S(C)(=O)=O)=C1)CCC2)

`REAL300000037858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037858 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 40, 40, 37, 37, 37, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 37, 37, 37, 37, 7, 1, 1, 1, 3, 3, 3, 1, 37, 37, 37, 37, 37, 37] 55
rigid atoms, others: [32, 33, 37, 12, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 75
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: REAL300000037858 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 37, 37, 10, 37, 37, 55, 55, 55, 37, 1, 1, 1, 2, 2, 2, 10, 37, 37, 10, 55, 55, 55, 37, 1, 1, 1, 1, 1, 1] 55
rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 9, 10, 11, 40, 43, 41, 24, 25, 26, 42, 39] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 222
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037858 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037858
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037858/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037858
Building REAL300000037859
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037859'
/scratch/stefan/7769618/working/building/REAL300000037859 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037859

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037859/0 /scratch/stefan/7769618/working/building/REAL300000037859 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1038
`/scratch/stefan/7769618/working/3D/1038' -> `0.mol2'
Preparing input files

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

`REAL300000037859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037859 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 55, 55, 33, 19, 33, 33, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 6, 18, 25, 36, 32, 1, 1, 33, 55, 55, 55, 33, 33, 33, 12, 6, 1, 1, 18, 18, 25, 25, 1, 1, 33] 201
rigid atoms, others: [35, 36, 41, 42, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43])
total number of confs: 386
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: REAL300000037859 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 5, 5, 21, 21, 33, 33, 23, 33, 113, 139, 157, 167, 165, 33, 33, 1, 3, 3, 3, 1, 1, 1, 5, 21, 33, 33, 139, 139, 157, 157, 33, 33, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 26, 30, 31] set([0, 2, 3, 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: 477
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037859 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037859
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037859/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037859
Building REAL300000037860
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037860'
/scratch/stefan/7769618/working/building/REAL300000037860 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037860

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037860/0 /scratch/stefan/7769618/working/building/REAL300000037860 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1039
`/scratch/stefan/7769618/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)=C1)C(=O)[O-])

`REAL300000037860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037860 none CC(OC1=CC=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [134, 103, 32, 32, 32, 32, 32, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 134, 135, 135, 134, 134, 134, 134, 32, 32, 32, 13, 5, 1, 1, 1, 3, 3, 3, 1, 32] 201
rigid atoms, others: [36, 37, 38, 42, 11, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 43])
total number of confs: 347
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: REAL300000037860 none CC(OC1=CC=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 9, 8, 32, 32, 8, 32, 32, 51, 51, 51, 32, 1, 25, 32, 32, 25, 25, 25, 25, 1, 1, 1, 4, 8, 32, 32, 15, 51, 51, 51, 32, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 43, 23, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 327
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037860 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037860
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037860/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037860
Building REAL300000037861
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037861'
/scratch/stefan/7769618/working/building/REAL300000037861 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037861

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037861/0 /scratch/stefan/7769618/working/building/REAL300000037861 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1040
`/scratch/stefan/7769618/working/3D/1040' -> `0.mol2'
Preparing input files

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

`REAL300000037861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037861 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 31, 47, 47, 31, 29, 31, 31, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 17, 21, 37, 32, 1, 31, 47, 47, 47, 31, 31, 31, 10, 6, 1, 1, 1, 17, 17, 21, 21, 1, 31] 201
rigid atoms, others: [35, 36, 37, 42, 13, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 43])
total number of confs: 280
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: REAL300000037861 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 31, 31, 31, 31, 31, 89, 131, 147, 156, 155, 31, 1, 3, 3, 3, 1, 1, 1, 5, 13, 31, 31, 31, 131, 131, 147, 147, 31, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 26, 30, 31] set([0, 2, 3, 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: 459
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037861 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037861
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037861/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037861
Building REAL300000037862
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037862'
/scratch/stefan/7769618/working/building/REAL300000037862 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037862

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037862/0 /scratch/stefan/7769618/working/building/REAL300000037862 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1041
`/scratch/stefan/7769618/working/3D/1041' -> `0.mol2'
Preparing input files

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

`REAL300000037862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037862 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 27, 44, 44, 27, 25, 27, 27, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 21, 34, 34, 1, 27, 44, 44, 44, 26, 27, 27, 10, 6, 1, 1, 1, 21, 21, 1, 27] 201
rigid atoms, others: [34, 35, 36, 39, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40])
total number of confs: 269
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: REAL300000037862 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 27, 27, 27, 27, 27, 74, 119, 125, 125, 27, 1, 3, 3, 3, 1, 1, 1, 5, 12, 27, 27, 27, 119, 119, 27, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 40, 25, 29, 30, 31] set([0, 2, 3, 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: 368
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037862 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037862
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037862/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037862
Building REAL300000037863
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037863'
/scratch/stefan/7769618/working/building/REAL300000037863 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037863

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037863/0 /scratch/stefan/7769618/working/building/REAL300000037863 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1042
`/scratch/stefan/7769618/working/3D/1042' -> `0.mol2'
Preparing input files

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

`REAL300000037863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037863 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 51, 73, 73, 51, 51, 51, 51, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 73, 73, 73, 51, 51, 51, 25, 10, 1, 1, 1, 51] 73
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037863 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 51, 51, 51, 51, 51, 51, 51, 1, 3, 3, 3, 1, 1, 1, 7, 29, 51, 51, 51, 1] 73
rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037863 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037863
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037863/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037863
Building REAL300000037864
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037864'
/scratch/stefan/7769618/working/building/REAL300000037864 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037864

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037864/0 /scratch/stefan/7769618/working/building/REAL300000037864 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1043
`/scratch/stefan/7769618/working/3D/1043' -> `0.mol2'
Preparing input files

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

`REAL300000037864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037864 none CCC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 6, 1, 6, 6, 27, 27, 27, 56, 56, 46, 56, 56, 92, 92, 92, 56, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 27, 56, 56, 56, 92, 92, 92, 56, 1, 1, 1, 1] 105
rigid atoms, others: [2, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 427
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: REAL300000037864 none CCC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 28, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 56, 56, 28, 31, 56, 56, 56, 56, 44, 44, 44, 44, 44, 7, 1, 1, 1, 3, 3, 3, 1, 56, 56, 56, 56] 105
rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 11, 12, 16] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 340
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037864 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037864
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037864/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037864
Building REAL300000037865
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037865'
/scratch/stefan/7769618/working/building/REAL300000037865 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037865

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037865/0 /scratch/stefan/7769618/working/building/REAL300000037865 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1044
`/scratch/stefan/7769618/working/3D/1044' -> `0.mol2'
Preparing input files

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

`REAL300000037865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037865 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 51, 51, 17, 51, 51, 61, 61, 61, 51, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 17, 51, 51, 17, 61, 61, 61, 51, 1, 1, 1, 1] 61
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 219
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037865 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 51, 51, 51, 51, 51, 51, 57, 57, 25, 25, 25, 7, 1, 1, 1, 3, 3, 3, 1, 51, 51, 51, 51] 61
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 117
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037865 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037865
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037865/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037865
Building REAL300000037866
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037866'
/scratch/stefan/7769618/working/building/REAL300000037866 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037866

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037866/0 /scratch/stefan/7769618/working/building/REAL300000037866 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1045
`/scratch/stefan/7769618/working/3D/1045' -> `0.mol2'
Preparing input files

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

`REAL300000037866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037866 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 57, 57, 25, 57, 57, 99, 99, 99, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 56, 57, 25, 99, 99, 99, 57, 1, 1, 1, 2] 198
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40])
total number of confs: 444
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: REAL300000037866 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 29, 57, 57, 57, 57, 57, 57, 57, 57, 57, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 1, 57, 57, 57, 114] 198
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 213
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037866 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037866
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037866/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037866
Building REAL300000037867
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037867'
/scratch/stefan/7769618/working/building/REAL300000037867 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037867

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037867/0 /scratch/stefan/7769618/working/building/REAL300000037867 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1046
`/scratch/stefan/7769618/working/3D/1046' -> `0.mol2'
Preparing input files

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

`REAL300000037867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037867 none CCC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [35, 12, 1, 12, 12, 45, 45, 45, 88, 88, 45, 88, 88, 136, 136, 136, 88, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 35, 35, 35, 35, 35, 45, 88, 88, 45, 136, 136, 136, 88, 1, 1, 1] 154
rigid atoms, others: [2, 40, 41, 42, 17, 18, 19, 20, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 665
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: REAL300000037867 none CCC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [49, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 88, 88, 88, 88, 88, 88, 88, 88, 88, 49, 49, 49, 49, 49, 7, 1, 1, 1, 3, 3, 3, 1, 88, 88, 88] 154
rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 16, 39] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42])
total number of confs: 242
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037867 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037867
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037867/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037867
Building REAL300000037868
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037868'
/scratch/stefan/7769618/working/building/REAL300000037868 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037868

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037868/0 /scratch/stefan/7769618/working/building/REAL300000037868 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1047
`/scratch/stefan/7769618/working/3D/1047' -> `0.mol2'
Preparing input files

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

`REAL300000037868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037868 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 35, 43, 43, 35, 35, 35, 35, 15, 14, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 43, 43, 43, 35, 35, 35, 14, 6, 1, 1, 1, 1, 35] 43
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300000037868 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 3, 3, 3, 1, 1, 1, 7, 29, 35, 35, 35, 35, 1] 43
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 39, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037868 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037868/1 /scratch/stefan/7769618/working/building/REAL300000037868 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1048
`/scratch/stefan/7769618/working/3D/1048' -> `1.mol2'
Preparing input files

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

`REAL300000037868.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037868/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037868 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 67, 105, 105, 67, 51, 67, 67, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 105, 105, 105, 65, 67, 67, 30, 10, 1, 1, 1, 1, 65] 105
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 430
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037868 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 27, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 3, 3, 3, 1, 1, 1, 7, 27, 67, 67, 67, 67, 1] 105
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 39, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037868 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037868
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037868/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037868/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037868
Building REAL300000037869
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037869'
/scratch/stefan/7769618/working/building/REAL300000037869 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037869

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037869/0 /scratch/stefan/7769618/working/building/REAL300000037869 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1049
`/scratch/stefan/7769618/working/3D/1049' -> `0.mol2'
Preparing input files

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

`REAL300000037869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037869 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
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: [11, 1, 11, 11, 21, 21, 21, 46, 46, 21, 46, 46, 81, 81, 81, 46, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 21, 46, 46, 21, 81, 81, 81, 46, 1, 1, 1, 1] 81
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 365
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037869 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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]
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: [18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 18, 46, 46, 46, 46, 46, 46, 46, 46, 18, 18, 18, 7, 1, 1, 1, 3, 3, 3, 1, 46, 46, 46, 46] 81
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 84
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037869 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037869
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037869/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037869
Building REAL300000037870
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037870'
/scratch/stefan/7769618/working/building/REAL300000037870 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037870

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037870/0 /scratch/stefan/7769618/working/building/REAL300000037870 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1050
`/scratch/stefan/7769618/working/3D/1050' -> `0.mol2'
Preparing input files

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

`REAL300000037870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037870 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [87, 61, 87, 87, 61, 17, 61, 61, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 8, 20, 20, 1, 1, 61, 87, 87, 87, 17, 61, 61, 16, 5, 1, 8, 8, 61] 163
rigid atoms, others: [32, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35])
total number of confs: 395
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037870 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 31, 61, 61, 61, 111, 115, 115, 61, 61, 1, 3, 3, 3, 1, 1, 1, 7, 31, 61, 111, 111, 1] 163
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29] set([0, 2, 3, 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: 371
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037870 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037870
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037870/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037870
Building REAL300000037871
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037871'
/scratch/stefan/7769618/working/building/REAL300000037871 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037871

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037871/0 /scratch/stefan/7769618/working/building/REAL300000037871 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1051)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1051
`/scratch/stefan/7769618/working/3D/1051' -> `0.mol2'
Preparing input files

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

`REAL300000037871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037871 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 27, 27, 27, 85, 85, 27, 85, 85, 145, 145, 145, 85, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 27, 85, 85, 27, 145, 145, 145, 85, 1, 1, 1] 145
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 623
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037871 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 19, 85, 85, 85, 85, 85, 85, 85, 85, 85, 19, 19, 19, 7, 1, 1, 1, 3, 3, 3, 1, 85, 85, 85] 145
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39])
total number of confs: 127
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037871 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037871
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037871/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037871
Building REAL300000037872
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037872'
/scratch/stefan/7769618/working/building/REAL300000037872 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037872

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037872/0 /scratch/stefan/7769618/working/building/REAL300000037872 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1052)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1052
`/scratch/stefan/7769618/working/3D/1052' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)=C1)

`REAL300000037872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037872 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 52, 78, 78, 52, 22, 52, 52, 22, 22, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 78, 78, 78, 31, 52, 52, 21, 10, 1, 1, 52] 78
rigid atoms, others: [32, 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, 33])
total number of confs: 337
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037872 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 52, 52, 52, 52, 52, 52, 52, 1, 3, 3, 3, 1, 1, 1, 7, 23, 52, 52, 1] 78
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037872 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037872
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037872/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037872
Building REAL300000037873
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037873'
/scratch/stefan/7769618/working/building/REAL300000037873 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037873

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037873/0 /scratch/stefan/7769618/working/building/REAL300000037873 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1053)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1053
`/scratch/stefan/7769618/working/3D/1053' -> `0.mol2'
Preparing input files

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

`REAL300000037873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037873 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 29, 55, 55, 29, 28, 29, 29, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 55, 55, 55, 28, 29, 29, 18, 10, 1, 1, 1, 29] 55
rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
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: REAL300000037873 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 3, 3, 3, 1, 1, 1, 7, 21, 29, 29, 29, 1] 55
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 36, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037873 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037873
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037873/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037873
Building REAL300000037874
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037874'
/scratch/stefan/7769618/working/building/REAL300000037874 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037874

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037874/0 /scratch/stefan/7769618/working/building/REAL300000037874 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1054)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1054
`/scratch/stefan/7769618/working/3D/1054' -> `0.mol2'
Preparing input files

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

`REAL300000037874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037874 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 32, 32, 32, 85, 85, 57, 85, 85, 149, 149, 149, 85, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 32, 85, 85, 85, 149, 149, 149, 85, 1, 2, 2, 2, 2, 2, 2] 149
rigid atoms, others: [1, 38, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 671
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: REAL300000037874 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 29, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 1, 85, 85, 85, 85, 85, 85, 85] 149
rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 15, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 129
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037874 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037874
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037874/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037874
Building REAL300000037875
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037875'
/scratch/stefan/7769618/working/building/REAL300000037875 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037875

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037875/0 /scratch/stefan/7769618/working/building/REAL300000037875 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1055)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1055
`/scratch/stefan/7769618/working/3D/1055' -> `0.mol2'
Preparing input files

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

`REAL300000037875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037875 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [55, 33, 55, 55, 33, 31, 33, 33, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 55, 55, 55, 31, 33, 33, 16, 8, 1, 1, 2, 1, 33] 110
rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037875 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 3, 3, 1, 1, 1, 7, 17, 33, 33, 66, 33, 1] 110
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 28, 29, 30, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037875 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037875
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037875/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037875
Building REAL300000037876
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037876'
/scratch/stefan/7769618/working/building/REAL300000037876 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037876

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037876/0 /scratch/stefan/7769618/working/building/REAL300000037876 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1056)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1056
`/scratch/stefan/7769618/working/3D/1056' -> `0.mol2'
Preparing input files

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

`REAL300000037876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037876 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 48, 48, 48, 48, 48, 77, 77, 77, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 48, 48, 48, 77, 77, 77, 48, 1, 1, 1, 2, 2, 2] 77
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 280
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: REAL300000037876 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 24, 24, 24, 7, 1, 1, 1, 3, 3, 3, 1, 48, 48, 48, 48, 48, 48] 77
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 89
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037876 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037876
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037876/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037876
Building REAL300000037877
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037877'
/scratch/stefan/7769618/working/building/REAL300000037877 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037877

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037877/0 /scratch/stefan/7769618/working/building/REAL300000037877 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1057)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1057
`/scratch/stefan/7769618/working/3D/1057' -> `0.mol2'
Preparing input files

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

`REAL300000037877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037877 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 8, 8, 8, 17, 17, 8, 17, 17, 31, 31, 31, 17, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 17, 17, 12, 31, 31, 31, 17, 1, 1] 31
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037877 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 7, 1, 1, 1, 3, 3, 3, 1, 17, 17] 31
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 15, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36])
total number of confs: 45
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037877 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037877
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037877/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037877
Building REAL300000037878
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037878'
/scratch/stefan/7769618/working/building/REAL300000037878 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037878

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037878/0 /scratch/stefan/7769618/working/building/REAL300000037878 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1058)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1058
`/scratch/stefan/7769618/working/3D/1058' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)C=C1)C(=O)[O-])

`REAL300000037878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037878 none CC(OC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [131, 105, 37, 37, 61, 61, 22, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 61, 61, 131, 137, 137, 131, 131, 131, 131, 61, 61, 22, 7, 1, 1, 1, 3, 3, 3, 1, 61, 61] 201
rigid atoms, others: [35, 36, 37, 41, 10, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 42, 43])
total number of confs: 409
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037878 none CC(OC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 61, 61, 59, 61, 61, 97, 97, 97, 61, 1, 1, 13, 20, 20, 13, 13, 13, 13, 1, 1, 7, 20, 61, 61, 61, 97, 97, 97, 61, 1, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 42, 43, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 398
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037878 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037878
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037878/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037878
Building REAL300000037879
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037879'
/scratch/stefan/7769618/working/building/REAL300000037879 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037879

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037879/0 /scratch/stefan/7769618/working/building/REAL300000037879 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1059)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1059
`/scratch/stefan/7769618/working/3D/1059' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)=C1)

`REAL300000037879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037879 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 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, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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]
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, 15, 29, 29, 15, 7, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 15, 29, 29, 29, 7, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15] 29
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 43])
total number of confs: 137
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: REAL300000037879 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 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, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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]
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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 3, 3, 3, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 29
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 26, 30, 31] set([0, 2, 3, 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: 41
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037879 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037879
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037879/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037879
Building REAL300000037880
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037880'
/scratch/stefan/7769618/working/building/REAL300000037880 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037880

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037880/0 /scratch/stefan/7769618/working/building/REAL300000037880 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1060)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1060
`/scratch/stefan/7769618/working/3D/1060' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1)

`REAL300000037880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037880 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [124, 78, 124, 124, 78, 31, 78, 78, 30, 31, 31, 9, 9, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 1, 1, 1, 78, 124, 124, 124, 31, 78, 78, 31, 9, 1, 7, 7, 1, 1, 1, 1, 78] 201
rigid atoms, others: [36, 39, 40, 41, 42, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43])
total number of confs: 554
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037880 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 5, 5, 27, 27, 78, 78, 78, 145, 161, 161, 78, 78, 78, 78, 78, 78, 1, 3, 3, 3, 1, 1, 1, 5, 27, 78, 145, 145, 78, 78, 78, 78, 1] 201
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 33, 27, 31] set([0, 2, 3, 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])
total number of confs: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037880 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037880
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037880/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037880
Building REAL300000037881
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037881'
/scratch/stefan/7769618/working/building/REAL300000037881 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037881

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037881/0 /scratch/stefan/7769618/working/building/REAL300000037881 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1061)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1061
`/scratch/stefan/7769618/working/3D/1061' -> `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=CC(S(C)(=O)=O)=C2)N1)

`REAL300000037881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037881 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 39, 39, 29, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 29, 29, 29, 29, 29, 25, 7, 1, 1, 1, 3, 3, 3, 1, 29] 51
rigid atoms, others: [32, 36, 11, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037881 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 29, 29, 8, 29, 29, 51, 51, 51, 29, 1, 2, 2, 2, 1, 4, 8, 29, 29, 8, 51, 51, 51, 29, 1] 51
rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037881 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037881
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037881/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037881
Building REAL300000037882
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037882'
/scratch/stefan/7769618/working/building/REAL300000037882 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037882

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037882/0 /scratch/stefan/7769618/working/building/REAL300000037882 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1062)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1062
`/scratch/stefan/7769618/working/3D/1062' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1)

`REAL300000037882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037882 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 34, 46, 46, 34, 23, 34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 46, 46, 46, 32, 34, 34, 9, 1, 1, 1, 1, 1, 34] 46
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 33])
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: REAL300000037882 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 34, 34, 34, 36, 36, 34, 1, 3, 3, 3, 1, 1, 1, 7, 34, 34, 34, 34, 34, 1] 46
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 20, 24, 25, 26] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037882 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037882
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037882/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037882
Building REAL300000037883
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037883'
/scratch/stefan/7769618/working/building/REAL300000037883 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037883

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037883/0 /scratch/stefan/7769618/working/building/REAL300000037883 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1063)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1063
`/scratch/stefan/7769618/working/3D/1063' -> `0.mol2'
Preparing input files

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

`REAL300000037883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037883 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 35, 59, 59, 35, 35, 35, 35, 17, 16, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 59, 59, 59, 35, 35, 35, 16, 8, 1, 1, 1, 1, 35] 59
rigid atoms, others: [32, 33, 34, 35, 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, 36])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037883 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 1, 3, 3, 3, 1, 1, 1, 7, 19, 35, 35, 35, 35, 1] 59
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 2, 3, 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: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037883 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037883
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037883/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037883
Building REAL300000037884
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037884'
/scratch/stefan/7769618/working/building/REAL300000037884 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037884

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037884/0 /scratch/stefan/7769618/working/building/REAL300000037884 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1064)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1064
`/scratch/stefan/7769618/working/3D/1064' -> `0.mol2'
Preparing input files

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

`REAL300000037884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037884 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 43, 43, 17, 43, 43, 77, 77, 77, 43, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 17, 43, 43, 28, 77, 77, 77, 43, 1, 1] 77
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 365
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037884 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 19, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 7, 1, 1, 1, 3, 3, 3, 1, 43, 43] 77
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 15, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36])
total number of confs: 77
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037884 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037884
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037884/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037884
Building REAL300000037885
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037885'
/scratch/stefan/7769618/working/building/REAL300000037885 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037885

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037885/0 /scratch/stefan/7769618/working/building/REAL300000037885 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1065)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1065
`/scratch/stefan/7769618/working/3D/1065' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1)

`REAL300000037885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037885 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [54, 29, 54, 54, 29, 6, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 6, 6, 1, 6, 6, 1, 29, 54, 54, 54, 6, 29, 29, 6, 1, 1, 6, 6, 1, 6, 6, 1, 1, 29] 68
rigid atoms, others: [34, 35, 41, 42, 11, 12, 13, 14, 15, 16, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43])
total number of confs: 246
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037885 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 39, 68, 68, 39, 15, 39, 39, 15, 15, 15, 6, 6, 6, 6, 1, 6, 8, 8, 1, 1, 1, 1, 1, 1, 6, 39, 68, 68, 68, 15, 39, 39, 15, 6, 6, 1, 1, 1, 1, 1, 6, 6, 39] 68
rigid atoms, others: [36, 37, 38, 39, 40, 15, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 295
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037885 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 29, 29, 41, 41, 29, 39, 39, 29, 39, 39, 29, 1, 3, 3, 3, 1, 1, 1, 7, 29, 29, 39, 39, 29, 39, 39, 29, 29, 1] 68
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 26, 30, 31] set([0, 2, 3, 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: 147
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037885 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037885
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037885/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037885
Building REAL300000037886
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037886'
/scratch/stefan/7769618/working/building/REAL300000037886 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037886

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037886/0 /scratch/stefan/7769618/working/building/REAL300000037886 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1066)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1066
`/scratch/stefan/7769618/working/3D/1066' -> `0.mol2'
Preparing input files

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

`REAL300000037886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037886 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 46, 46, 25, 46, 46, 74, 74, 74, 46, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 6, 6, 6, 16, 46, 46, 46, 74, 74, 74, 46, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 102
rigid atoms, others: [1, 39, 40, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 388
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: REAL300000037886 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 29, 46, 46, 46, 46, 46, 79, 90, 90, 46, 46, 46, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 1, 46, 46, 79, 79, 46, 46, 46, 46, 46, 46] 102
rigid atoms, others: [32, 33, 34, 4, 38, 6, 7, 8, 9, 10, 11, 15] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 313
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037886 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037886
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037886/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037886
Building REAL300000037887
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037887'
/scratch/stefan/7769618/working/building/REAL300000037887 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037887

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037887/0 /scratch/stefan/7769618/working/building/REAL300000037887 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1067)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1067
`/scratch/stefan/7769618/working/3D/1067' -> `0.mol2'
Preparing input files

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

`REAL300000037887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037887 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 69, 73, 91, 89, 117, 165, 167, 167, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 21, 21, 21, 69, 69, 91, 91, 91, 91, 105, 105, 121, 121, 165, 165, 5, 1, 1, 1, 3, 3, 3, 1] 201
rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46])
total number of confs: 994
number of broken/clashed sets: 177
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037887 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037887
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037887/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037887
Building REAL300000037888
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037888'
/scratch/stefan/7769618/working/building/REAL300000037888 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037888

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037888/0 /scratch/stefan/7769618/working/building/REAL300000037888 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1068)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1068
`/scratch/stefan/7769618/working/3D/1068' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)CCC1CC(=O)[O-])

`REAL300000037888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037888 none CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 32, 50, 51, 51, 32, 32, 32, 32, 7, 1, 1, 1, 3, 3, 3, 1, 32, 32, 32, 32, 32, 50, 50] 85
rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
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: REAL300000037888 none CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 57, 57, 57, 32, 1, 1, 1, 1, 8, 12, 12, 2, 2, 2, 1, 8, 32, 32, 32, 57, 57, 57, 32, 1, 1, 1, 1, 1, 8, 8] 85
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 17, 18, 19, 20, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037888 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037888
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037888/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037888
Building REAL300000037889
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037889'
/scratch/stefan/7769618/working/building/REAL300000037889 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037889

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037889/0 /scratch/stefan/7769618/working/building/REAL300000037889 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1069)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1069
`/scratch/stefan/7769618/working/3D/1069' -> `0.mol2'
Preparing input files

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

`REAL300000037889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037889 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 67, 67, 37, 67, 67, 91, 91, 91, 67, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 67, 67, 37, 91, 91, 91, 67, 1, 1] 91
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 358
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037889 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 67, 67, 67, 67, 67, 67, 67, 27, 27, 27, 7, 1, 1, 1, 3, 3, 3, 1, 67, 67] 91
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 15, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037889 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037889
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037889/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037889
Building REAL300000037890
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037890'
/scratch/stefan/7769618/working/building/REAL300000037890 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037890

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037890/0 /scratch/stefan/7769618/working/building/REAL300000037890 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1070)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1070
`/scratch/stefan/7769618/working/3D/1070' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)CCC(C(=O)[O-])C1(C)C)

`REAL300000037890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037890 none CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 3, 3, 3, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 25
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 16, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 45
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: REAL300000037890 none CC1C(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
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, 8, 8, 8, 19, 19, 8, 19, 19, 25, 25, 25, 19, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 8, 19, 19, 8, 25, 25, 25, 19, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 25
rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 40, 41, 42, 17, 18, 19, 20, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48])
total number of confs: 115
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037890 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037890
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037890/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037890
Building REAL300000037891
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037891'
/scratch/stefan/7769618/working/building/REAL300000037891 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037891

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037891/0 /scratch/stefan/7769618/working/building/REAL300000037891 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1071)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1071
`/scratch/stefan/7769618/working/3D/1071' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=CC(S(C)(=O)=O)=C1)

`REAL300000037891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037891 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 31, 37, 37, 31, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 1, 1, 1, 3, 3, 3, 1] 52
rigid atoms, others: [36, 37, 38, 42, 12, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 81
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: REAL300000037891 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
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, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 8, 31, 31, 52, 52, 52, 31, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 8, 52, 52, 52, 31] 52
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 11, 34, 32, 27, 28, 29, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 222
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037891 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037891
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037891/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037891
Building REAL300000037892
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037892'
/scratch/stefan/7769618/working/building/REAL300000037892 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037892

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037892/0 /scratch/stefan/7769618/working/building/REAL300000037892 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1072)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1072
`/scratch/stefan/7769618/working/3D/1072' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)CCC1C(=O)[O-])

`REAL300000037892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037892 none CC1CC(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 3, 3, 3, 1, 24, 24, 24, 24, 24] 26
rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 50
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: REAL300000037892 none CC1CC(=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
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, 9, 9, 9, 24, 24, 9, 24, 24, 26, 26, 26, 24, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 9, 24, 24, 9, 26, 26, 26, 24, 1, 1, 1, 1, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 18, 19, 20, 21, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 92
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037892 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037892
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037892/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037892
Building REAL300000037893
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037893'
/scratch/stefan/7769618/working/building/REAL300000037893 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037893

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037893/0 /scratch/stefan/7769618/working/building/REAL300000037893 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1073)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1073
`/scratch/stefan/7769618/working/3D/1073' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)=C1)

`REAL300000037893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037893 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 27, 27, 16, 7, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 27, 27, 27, 13, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 27
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 33, 32, 26, 27, 28, 29, 30, 31])
total number of confs: 129
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: REAL300000037893 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 3, 3, 3, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 27
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 43, 26, 30, 31] set([0, 2, 3, 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: 42
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037893 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037893
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037893/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037893
Building REAL300000037894
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037894'
/scratch/stefan/7769618/working/building/REAL300000037894 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037894

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037894/0 /scratch/stefan/7769618/working/building/REAL300000037894 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1074)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1074
`/scratch/stefan/7769618/working/3D/1074' -> `0.mol2'
Preparing input files

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

`REAL300000037894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037894 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 63, 63, 41, 18, 41, 41, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 63, 63, 63, 18, 41, 41, 18, 8, 1, 1, 1, 41] 63
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
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: REAL300000037894 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 41, 41, 41, 41, 41, 41, 41, 1, 3, 3, 3, 1, 1, 1, 7, 23, 41, 41, 41, 1] 63
rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037894 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037894
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037894/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037894
Building REAL300000037895
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037895'
/scratch/stefan/7769618/working/building/REAL300000037895 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037895

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037895/0 /scratch/stefan/7769618/working/building/REAL300000037895 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1075)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1075
`/scratch/stefan/7769618/working/3D/1075' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037895 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 58, 62, 62, 62, 62, 62, 62, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 23, 23, 23, 58, 58, 62, 62, 62, 62, 62, 62, 7, 1, 1, 1, 3, 3, 3, 1] 109
rigid atoms, others: [36, 37, 38, 42, 12, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 217
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037895 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
109  conformations in input
total number of sets (complete confs): 109
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, 62, 62, 28, 62, 62, 109, 109, 109, 62, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 28, 62, 62, 28, 109, 109, 109, 62] 109
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 500
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037895 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037895
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037895/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037895
Building REAL300000037896
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037896'
/scratch/stefan/7769618/working/building/REAL300000037896 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037896

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037896/0 /scratch/stefan/7769618/working/building/REAL300000037896 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1076)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1076
`/scratch/stefan/7769618/working/3D/1076' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037896 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [78, 75, 79, 79, 79, 79, 79, 79, 79, 79, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 79, 79, 79, 79, 79, 79, 79, 79, 25, 7, 1, 1, 1, 3, 3, 3, 1] 95
rigid atoms, others: [36, 37, 38, 42, 14, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037896 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 38, 38, 38, 79, 79, 38, 79, 79, 95, 95, 95, 79, 2, 2, 2, 1, 2, 2, 2, 1, 13, 38, 76, 79, 38, 95, 95, 95, 79] 95
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037896 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037896
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037896/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037896
Building REAL300000037897
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037897'
/scratch/stefan/7769618/working/building/REAL300000037897 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037897

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037897/0 /scratch/stefan/7769618/working/building/REAL300000037897 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1077)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1077
`/scratch/stefan/7769618/working/3D/1077' -> `0.mol2'
Preparing input files

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

`REAL300000037897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037897 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 32, 51, 51, 32, 15, 32, 32, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 32, 51, 51, 51, 15, 32, 32, 15, 7, 1, 1, 1, 32] 51
rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037897 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 3, 3, 3, 1, 1, 1, 7, 15, 32, 32, 32, 1] 51
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 36, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037897 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037897
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037897/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037897
Building REAL300000037898
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037898'
/scratch/stefan/7769618/working/building/REAL300000037898 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037898

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037898/0 /scratch/stefan/7769618/working/building/REAL300000037898 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1078)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1078
`/scratch/stefan/7769618/working/3D/1078' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037898 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 25, 25, 25, 17, 7, 1, 1, 1, 3, 3, 3, 1] 39
rigid atoms, others: [32, 36, 12, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35])
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: REAL300000037898 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 12, 12, 12, 25, 25, 12, 25, 25, 39, 39, 39, 25, 2, 2, 2, 1, 6, 12, 25, 25, 12, 39, 39, 39, 25] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037898 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037898
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037898/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037898
Building REAL300000037899
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037899'
/scratch/stefan/7769618/working/building/REAL300000037899 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037899

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037899/0 /scratch/stefan/7769618/working/building/REAL300000037899 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1079)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1079
`/scratch/stefan/7769618/working/3D/1079' -> `0.mol2'
Preparing input files

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

`REAL300000037899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037899 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 65, 105, 105, 65, 18, 65, 65, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 65, 105, 105, 105, 18, 65, 65, 18, 8, 1, 1, 1, 65] 105
rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 431
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037899 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 33, 65, 65, 65, 65, 69, 69, 65, 65, 65, 1, 3, 3, 3, 1, 1, 1, 7, 33, 65, 65, 65, 1] 105
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 36, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037899 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037899
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037899/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037899
Building REAL300000037900
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037900'
/scratch/stefan/7769618/working/building/REAL300000037900 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037900

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037900/0 /scratch/stefan/7769618/working/building/REAL300000037900 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1080)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1080
`/scratch/stefan/7769618/working/3D/1080' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1)

`REAL300000037900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037900 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 118, 118, 74, 23, 74, 74, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 31, 31, 1, 74, 118, 118, 118, 23, 74, 74, 23, 7, 1, 1, 12, 12, 74] 201
rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37])
total number of confs: 561
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037900 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 7, 7, 7, 33, 33, 74, 74, 74, 74, 140, 140, 156, 156, 74, 1, 3, 3, 3, 1, 1, 1, 7, 33, 74, 74, 140, 140, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 28, 29, 30, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037900 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037900
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037900/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037900
Building REAL300000037901
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037901'
/scratch/stefan/7769618/working/building/REAL300000037901 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037901

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037901/0 /scratch/stefan/7769618/working/building/REAL300000037901 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1081)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1081
`/scratch/stefan/7769618/working/3D/1081' -> `0.mol2'
Preparing input files

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

`REAL300000037901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037901 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 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]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 33, 33, 21, 5, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 33, 33, 33, 5, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 21] 33
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 40])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037901 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 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]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 3, 3, 3, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 1] 33
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 40, 25, 29, 30, 31] set([0, 2, 3, 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: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037901 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037901
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037901/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037901
Building REAL300000037902
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037902'
/scratch/stefan/7769618/working/building/REAL300000037902 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037902

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037902/0 /scratch/stefan/7769618/working/building/REAL300000037902 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1082)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1082
`/scratch/stefan/7769618/working/3D/1082' -> `0.mol2'
Preparing input files

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

`REAL300000037902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037902 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 19, 19, 19, 43, 43, 19, 43, 43, 79, 79, 79, 43, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 19, 43, 43, 31, 79, 79, 79, 43, 1, 1, 1] 79
rigid atoms, others: [1, 36, 37, 38, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 379
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037902 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 19, 43, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 7, 1, 1, 1, 3, 3, 3, 1, 43, 43, 43] 79
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38])
total number of confs: 79
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037902 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037902
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037902/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037902
Building REAL300000037903
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037903'
/scratch/stefan/7769618/working/building/REAL300000037903 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037903

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037903/0 /scratch/stefan/7769618/working/building/REAL300000037903 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1083)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1083
`/scratch/stefan/7769618/working/3D/1083' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1)

`REAL300000037903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037903 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 29, 53, 53, 29, 20, 29, 29, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 53, 53, 53, 20, 29, 29, 20, 6, 1, 1, 1, 1, 1, 29] 53
rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40])
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: REAL300000037903 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 3, 3, 3, 1, 1, 1, 7, 25, 29, 29, 29, 29, 29, 1] 53
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 40, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037903 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037903
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037903/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037903
Building REAL300000037904
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037904'
/scratch/stefan/7769618/working/building/REAL300000037904 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037904

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037904/0 /scratch/stefan/7769618/working/building/REAL300000037904 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1084)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1084
`/scratch/stefan/7769618/working/3D/1084' -> `0.mol2'
Preparing input files

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

`REAL300000037904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037904 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 69, 69, 45, 23, 45, 45, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 69, 69, 69, 35, 45, 45, 23, 11, 1, 1, 1, 45] 69
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 321
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037904 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 45, 45, 45, 45, 45, 45, 45, 43, 1, 3, 3, 3, 1, 1, 1, 7, 17, 45, 45, 45, 1] 69
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29] set([0, 2, 3, 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: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037904 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037904
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037904/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037904
Building REAL300000037905
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037905'
/scratch/stefan/7769618/working/building/REAL300000037905 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037905

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037905/0 /scratch/stefan/7769618/working/building/REAL300000037905 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1085)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1085
`/scratch/stefan/7769618/working/3D/1085' -> `0.mol2'
Preparing input files

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

`REAL300000037905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037905 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [93, 54, 93, 93, 54, 54, 54, 54, 19, 19, 20, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 54, 93, 93, 93, 54, 54, 54, 19, 9, 1, 1, 2, 1, 54] 186
rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37])
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: REAL300000037905 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 54, 54, 54, 54, 56, 56, 54, 54, 50, 1, 3, 3, 3, 1, 1, 1, 7, 24, 54, 54, 108, 54, 1] 186
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 28, 29, 30, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037905 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037905
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037905/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037905
Building REAL300000037906
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037906'
/scratch/stefan/7769618/working/building/REAL300000037906 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037906

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037906/0 /scratch/stefan/7769618/working/building/REAL300000037906 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1086)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1086
`/scratch/stefan/7769618/working/3D/1086' -> `0.mol2'
Preparing input files

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

`REAL300000037906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037906 none CC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 21, 7, 1, 1, 1, 3, 3, 3, 1, 57] 87
rigid atoms, others: [32, 33, 34, 38, 8, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037906 none CC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 22, 23, 22, 57, 57, 54, 57, 57, 87, 87, 87, 57, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 22, 57, 57, 55, 87, 87, 87, 57, 1] 87
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037906 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037906
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037906/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037906
Building REAL300000037907
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037907'
/scratch/stefan/7769618/working/building/REAL300000037907 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037907

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037907/0 /scratch/stefan/7769618/working/building/REAL300000037907 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1087)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1087
`/scratch/stefan/7769618/working/3D/1087' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1)

`REAL300000037907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037907 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 93, 143, 143, 93, 91, 93, 93, 36, 36, 37, 12, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 93, 143, 143, 143, 93, 93, 93, 36, 12, 1, 93] 143
rigid atoms, others: [32, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33])
total number of confs: 489
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037907 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 93, 93, 93, 99, 99, 93, 93, 93, 1, 3, 3, 3, 1, 1, 1, 7, 29, 93, 1] 143
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 33, 27, 28, 29] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037907 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037907
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037907/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037907
Building REAL300000037908
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037908'
/scratch/stefan/7769618/working/building/REAL300000037908 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037908

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037908/0 /scratch/stefan/7769618/working/building/REAL300000037908 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1088)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1088
`/scratch/stefan/7769618/working/3D/1088' -> `0.mol2'
Preparing input files

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

`REAL300000037908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037908 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 47, 47, 47, 47, 47, 71, 71, 71, 47, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 25, 46, 47, 47, 71, 71, 71, 47, 1, 1, 1, 2, 2, 2] 71
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 254
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037908 none CC(=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 47, 47, 37, 45, 47, 47, 47, 47, 47, 25, 25, 25, 7, 1, 1, 1, 3, 3, 3, 1, 47, 47, 47, 47, 47, 47] 71
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 139
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037908 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037908
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037908/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037908
Building REAL300000037909
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037909'
/scratch/stefan/7769618/working/building/REAL300000037909 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037909

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037909/0 /scratch/stefan/7769618/working/building/REAL300000037909 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1089)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1089
`/scratch/stefan/7769618/working/3D/1089' -> `0.mol2'
Preparing input files

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

`REAL300000037909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037909 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 29, 47, 47, 29, 29, 29, 29, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 29, 47, 47, 47, 29, 29, 29, 12, 6, 1, 1, 29] 47
rigid atoms, others: [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, 32, 35])
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: REAL300000037909 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 29, 29, 29, 29, 29, 29, 29, 31, 31, 1, 3, 3, 3, 1, 1, 1, 7, 11, 29, 29, 1] 47
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 24, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037909 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037909
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037909/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037909
Building REAL300000037910
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037910'
/scratch/stefan/7769618/working/building/REAL300000037910 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037910

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037910/0 /scratch/stefan/7769618/working/building/REAL300000037910 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1090)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1090
`/scratch/stefan/7769618/working/3D/1090' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037910 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 43, 43, 43, 43, 27, 7, 1, 1, 1, 3, 3, 3, 1] 64
rigid atoms, others: [32, 36, 12, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35])
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: REAL300000037910 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 43, 43, 17, 43, 43, 64, 64, 64, 43, 2, 2, 2, 1, 6, 17, 43, 43, 17, 64, 64, 64, 43] 64
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037910 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037910
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037910/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037910
Building REAL300000037911
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037911'
/scratch/stefan/7769618/working/building/REAL300000037911 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037911

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037911/0 /scratch/stefan/7769618/working/building/REAL300000037911 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1091)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1091
`/scratch/stefan/7769618/working/3D/1091' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037911 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 33, 33, 21, 7, 1, 1, 1, 3, 3, 3, 1] 53
rigid atoms, others: [32, 33, 37, 12, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
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: REAL300000037911 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 16, 16, 16, 33, 33, 16, 33, 33, 53, 53, 53, 33, 2, 2, 2, 1, 1, 6, 16, 33, 33, 16, 53, 53, 53, 33] 53
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 27, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037911 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037911
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037911/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037911
Building REAL300000037912
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037912'
/scratch/stefan/7769618/working/building/REAL300000037912 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037912

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037912/0 /scratch/stefan/7769618/working/building/REAL300000037912 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1092)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1092
`/scratch/stefan/7769618/working/3D/1092' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037912 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [31, 30, 31, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 31, 31, 30, 30, 30, 17, 5, 1, 1, 1, 3, 3, 3, 1] 57
rigid atoms, others: [38, 39, 40, 44, 15, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43])
total number of confs: 58
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: REAL300000037912 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 20, 20, 20, 30, 30, 21, 30, 30, 57, 57, 57, 30, 4, 4, 4, 4, 4, 4, 1, 1, 1, 12, 20, 30, 30, 24, 57, 57, 57, 30] 57
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 35, 7] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 272
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037912 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037912
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037912/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037912
Building REAL300000037913
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037913'
/scratch/stefan/7769618/working/building/REAL300000037913 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037913

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037913/0 /scratch/stefan/7769618/working/building/REAL300000037913 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1093)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1093
`/scratch/stefan/7769618/working/3D/1093' -> `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=CC(S(C)(=O)=O)=C2)O1)

`REAL300000037913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037913 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 86, 86, 78, 34, 34, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 78, 78, 78, 78, 78, 34, 7, 1, 1, 1, 3, 3, 3, 1] 122
rigid atoms, others: [32, 36, 11, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 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: REAL300000037913 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 31, 31, 31, 78, 78, 31, 78, 78, 122, 122, 122, 78, 1, 2, 2, 2, 1, 12, 31, 78, 78, 31, 122, 122, 122, 78] 122
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 499
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037913 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037913
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037913/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037913
Building REAL300000037914
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037914'
/scratch/stefan/7769618/working/building/REAL300000037914 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037914

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037914/0 /scratch/stefan/7769618/working/building/REAL300000037914 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1094)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1094
`/scratch/stefan/7769618/working/3D/1094' -> `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=CC(S(C)(=O)=O)=C2)S1)

`REAL300000037914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037914 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [71, 43, 43, 43, 43, 43, 53, 53, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 43, 71, 71, 71, 71, 71, 43, 21, 7, 1, 1, 1, 3, 3, 3, 1] 113
rigid atoms, others: [33, 34, 35, 39, 12, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037914 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 13, 13, 13, 43, 43, 13, 43, 43, 71, 71, 71, 43, 1, 9, 9, 9, 8, 8, 1, 5, 13, 43, 43, 13, 71, 71, 71, 43] 113
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 24, 30] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037914 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037914
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037914/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037914
Building REAL300000037915
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037915'
/scratch/stefan/7769618/working/building/REAL300000037915 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037915

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037915/0 /scratch/stefan/7769618/working/building/REAL300000037915 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1095)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1095
`/scratch/stefan/7769618/working/3D/1095' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037915 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 134, 134, 134, 134, 134, 134, 134, 134, 134, 30, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 144, 144, 144, 134, 134, 134, 30, 7, 1, 1, 1, 3, 3, 3, 1] 201
rigid atoms, others: [34, 35, 36, 40, 14, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037915 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 50, 50, 50, 134, 134, 50, 134, 134, 201, 201, 201, 134, 3, 3, 3, 1, 1, 1, 12, 50, 131, 134, 50, 201, 201, 201, 134] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 29, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 789
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037915 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037915
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037915/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037915
Building REAL300000037916
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037916'
/scratch/stefan/7769618/working/building/REAL300000037916 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037916

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037916/0 /scratch/stefan/7769618/working/building/REAL300000037916 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1096)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1096
`/scratch/stefan/7769618/working/3D/1096' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)=C1)

`REAL300000037916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037916 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 28, 28, 19, 6, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 28, 28, 28, 6, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19] 28
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 42])
total number of confs: 112
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: REAL300000037916 none CS(=O)(=O)C1=CC=CC(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 3, 3, 3, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 1] 28
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 42, 26, 30, 31] set([0, 2, 3, 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: 43
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037916 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037916
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037916/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037916
Building REAL300000037917
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037917'
/scratch/stefan/7769618/working/building/REAL300000037917 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037917

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037917/0 /scratch/stefan/7769618/working/building/REAL300000037917 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1097)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1097
`/scratch/stefan/7769618/working/3D/1097' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1)

`REAL300000037917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037917 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 49, 77, 77, 49, 23, 49, 49, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 77, 77, 77, 23, 49, 49, 23, 9, 1, 1, 49] 77
rigid atoms, others: [32, 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, 33])
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: REAL300000037917 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 49, 49, 49, 49, 49, 49, 49, 1, 3, 3, 3, 1, 1, 1, 7, 23, 49, 49, 1] 77
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037917 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037917
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037917/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037917
Building REAL300000037918
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037918'
/scratch/stefan/7769618/working/building/REAL300000037918 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037918

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037918/0 /scratch/stefan/7769618/working/building/REAL300000037918 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1098)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1098
`/scratch/stefan/7769618/working/3D/1098' -> `0.mol2'
Preparing input files

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

`REAL300000037918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037918 none CC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 25, 27, 27, 25, 25, 25, 25, 25, 25, 11, 7, 1, 1, 1, 3, 3, 3, 1, 25] 41
rigid atoms, others: [32, 33, 34, 38, 8, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39])
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: REAL300000037918 none CC1=CC=C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 25, 25, 25, 25, 25, 41, 41, 41, 25, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 10, 25, 25, 25, 41, 41, 41, 25, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037918 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037918
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037918/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037918
Building REAL300000037919
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037919'
/scratch/stefan/7769618/working/building/REAL300000037919 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037919

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037919/0 /scratch/stefan/7769618/working/building/REAL300000037919 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1099)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1099
`/scratch/stefan/7769618/working/3D/1099' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=O)=C2)=CC=C1C(=O)[O-])

`REAL300000037919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037919 none COC1=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [123, 85, 85, 85, 38, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 85, 85, 85, 85, 139, 139, 123, 123, 123, 85, 38, 7, 1, 1, 1, 3, 3, 3, 1, 85, 85] 201
rigid atoms, others: [32, 33, 34, 38, 8, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40])
total number of confs: 432
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037919 none COC1=CC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 30, 30, 30, 85, 85, 42, 85, 85, 141, 141, 141, 85, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 8, 30, 85, 85, 45, 141, 141, 141, 85, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037919 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037919
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037919/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037919
Building REAL300000037920
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037920'
/scratch/stefan/7769618/working/building/REAL300000037920 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037920

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037920/0 /scratch/stefan/7769618/working/building/REAL300000037920 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1100)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1100
`/scratch/stefan/7769618/working/3D/1100' -> `0.mol2'
Preparing input files

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

`REAL300000037920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037920 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 43, 53, 53, 43, 41, 43, 43, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 53, 53, 53, 41, 43, 43, 20, 6, 1, 1, 43] 53
rigid atoms, others: [34, 35, 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, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
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: REAL300000037920 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 43, 43, 43, 31, 32, 43, 43, 43, 43, 43, 1, 3, 3, 3, 1, 1, 1, 7, 21, 43, 43, 1] 53
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 25, 36, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037920 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037920
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037920/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037920
Building REAL300000037921
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037921'
/scratch/stefan/7769618/working/building/REAL300000037921 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037921

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037921/0 /scratch/stefan/7769618/working/building/REAL300000037921 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1101)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1101
`/scratch/stefan/7769618/working/3D/1101' -> `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=CC(S(C)(=O)=O)=C2)=C1)

`REAL300000037921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037921 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 78, 78, 72, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 72, 72, 72, 72, 72, 31, 7, 1, 1, 1, 3, 3, 3, 1, 72] 114
rigid atoms, others: [32, 36, 11, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37])
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: REAL300000037921 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 28, 29, 28, 72, 72, 72, 72, 72, 114, 114, 114, 72, 1, 2, 2, 2, 1, 12, 28, 72, 72, 72, 114, 114, 114, 72, 1] 114
rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 396
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037921 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037921
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037921/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037921
Building REAL300000037922
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037922'
/scratch/stefan/7769618/working/building/REAL300000037922 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037922

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037922/0 /scratch/stefan/7769618/working/building/REAL300000037922 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1102)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1102
`/scratch/stefan/7769618/working/3D/1102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)=C1)

`REAL300000037922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037922 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 45, 45, 32, 32, 32, 32, 16, 16, 16, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 32, 45, 45, 45, 32, 32, 32, 16, 6, 1, 32] 45
rigid atoms, others: [32, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037922 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 1, 3, 3, 3, 1, 1, 1, 7, 17, 32, 1] 45
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 33, 27, 28, 29] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037922 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037922
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037922/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037922
Building REAL300000037923
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037923'
/scratch/stefan/7769618/working/building/REAL300000037923 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037923

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037923/0 /scratch/stefan/7769618/working/building/REAL300000037923 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1103)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1103
`/scratch/stefan/7769618/working/3D/1103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)=C1)

`REAL300000037923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037923 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 47, 47, 34, 17, 34, 34, 17, 17, 18, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 34, 47, 47, 47, 24, 34, 34, 17, 5, 1, 1, 34] 47
rigid atoms, others: [32, 13, 14, 15, 16, 19, 20, 21, 31] 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, 33])
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: REAL300000037923 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 34, 34, 34, 34, 34, 34, 34, 1, 3, 3, 3, 1, 1, 1, 7, 19, 34, 34, 1] 47
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037923 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037923
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037923/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037923
Building REAL300000037924
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037924'
/scratch/stefan/7769618/working/building/REAL300000037924 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037924

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037924/0 /scratch/stefan/7769618/working/building/REAL300000037924 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1104)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1104
`/scratch/stefan/7769618/working/3D/1104' -> `0.mol2'
Preparing input files

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

`REAL300000037924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037924 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 43, 65, 65, 43, 27, 43, 43, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 65, 65, 65, 36, 43, 43, 18, 8, 1, 1, 43] 65
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037924 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 7, 7, 7, 25, 25, 43, 43, 43, 43, 43, 43, 43, 1, 3, 3, 3, 1, 1, 1, 7, 25, 43, 43, 1] 65
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 22, 26, 27, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037924 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037924
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037924/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037924
Building REAL300000037925
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037925'
/scratch/stefan/7769618/working/building/REAL300000037925 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037925

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037925/0 /scratch/stefan/7769618/working/building/REAL300000037925 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1105)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1105
`/scratch/stefan/7769618/working/3D/1105' -> `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=CC(S(C)(=O)=O)=C2)=C1C(=O)[O-])

`REAL300000037925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037925 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [83, 53, 53, 53, 53, 53, 53, 35, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 53, 53, 77, 77, 83, 83, 83, 53, 53, 53, 53, 53, 35, 7, 1, 1, 1, 3, 3, 3, 1] 135
rigid atoms, others: [43, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037925 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 53, 53, 17, 53, 53, 93, 93, 93, 53, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 5, 17, 53, 53, 17, 93, 93, 93, 53] 135
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037925 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037925
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037925/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037925
Building REAL300000037926
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037926'
/scratch/stefan/7769618/working/building/REAL300000037926 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037926

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037926/0 /scratch/stefan/7769618/working/building/REAL300000037926 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1106)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1106
`/scratch/stefan/7769618/working/3D/1106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)=C1)

`REAL300000037926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037926 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 35, 61, 61, 35, 12, 35, 35, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 8, 18, 27, 21, 1, 35, 61, 61, 61, 21, 35, 35, 12, 4, 1, 1, 8, 8, 18, 18, 35] 201
rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 384
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037926 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 5, 5, 25, 25, 35, 35, 35, 35, 98, 129, 137, 129, 35, 1, 3, 3, 3, 1, 1, 1, 5, 25, 35, 35, 98, 98, 129, 129, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 39, 24, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037926 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037926
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037926/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037926
Building REAL300000037927
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037927'
/scratch/stefan/7769618/working/building/REAL300000037927 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037927

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037927/0 /scratch/stefan/7769618/working/building/REAL300000037927 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1107)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1107
`/scratch/stefan/7769618/working/3D/1107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1)

`REAL300000037927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037927 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 61, 77, 77, 61, 42, 61, 61, 25, 25, 25, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 61, 77, 77, 77, 42, 61, 61, 24, 12, 1, 1, 1, 1, 1, 61] 77
rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40])
total number of confs: 271
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037927 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 3, 3, 3, 1, 1, 1, 7, 23, 61, 61, 61, 61, 61, 1] 77
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 40, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037927 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037927
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037927/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037927
Building REAL300000037928
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037928'
/scratch/stefan/7769618/working/building/REAL300000037928 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037928

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037928/0 /scratch/stefan/7769618/working/building/REAL300000037928 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1108)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1108
`/scratch/stefan/7769618/working/3D/1108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1)

`REAL300000037928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037928 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 48, 71, 71, 48, 26, 48, 48, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 48, 71, 71, 71, 26, 48, 48, 26, 11, 1, 1, 1, 1, 48] 71
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
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: REAL300000037928 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 3, 3, 3, 1, 1, 1, 7, 23, 48, 48, 48, 48, 1] 71
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 39, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037928 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037928
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037928/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037928
Building REAL300000037929
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037929'
/scratch/stefan/7769618/working/building/REAL300000037929 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037929

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037929/0 /scratch/stefan/7769618/working/building/REAL300000037929 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1109)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1109
`/scratch/stefan/7769618/working/3D/1109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1)

`REAL300000037929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037929 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 37, 37, 23, 20, 23, 23, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 37, 37, 37, 20, 23, 23, 13, 5, 1, 1, 1, 1, 23] 37
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037929 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 3, 3, 3, 1, 1, 1, 7, 15, 23, 23, 23, 23, 1] 37
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 39, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037929 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037929
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037929/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037929
Building REAL300000037930
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037930'
/scratch/stefan/7769618/working/building/REAL300000037930 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037930

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037930/0 /scratch/stefan/7769618/working/building/REAL300000037930 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1110)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1110
`/scratch/stefan/7769618/working/3D/1110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])=C1)

`REAL300000037930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037930 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 39, 39, 23, 8, 23, 23, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 23, 39, 39, 39, 11, 23, 23, 8, 6, 1, 1, 1, 23] 39
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])
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: REAL300000037930 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 3, 3, 3, 1, 1, 1, 7, 11, 23, 23, 23, 1] 39
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 36, 28, 29, 30] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037930 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037930
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037930/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037930
Building REAL300000037931
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037931'
/scratch/stefan/7769618/working/building/REAL300000037931 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037931

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037931/0 /scratch/stefan/7769618/working/building/REAL300000037931 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1111)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1111
`/scratch/stefan/7769618/working/3D/1111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)=C1)

`REAL300000037931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037931 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 38, 65, 65, 38, 26, 38, 38, 16, 16, 16, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 38, 65, 65, 65, 38, 38, 38, 16, 7, 1, 1, 1, 1, 38] 65
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
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: REAL300000037931 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 7, 7, 7, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 3, 3, 3, 1, 1, 1, 7, 18, 38, 38, 38, 38, 1] 65
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 39, 26, 30, 31] set([0, 2, 3, 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])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037931 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037931
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037931/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037931
Building REAL300000037932
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037932'
/scratch/stefan/7769618/working/building/REAL300000037932 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037932

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037932/0 /scratch/stefan/7769618/working/building/REAL300000037932 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1112)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1112
`/scratch/stefan/7769618/working/3D/1112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])=C1)

`REAL300000037932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037932 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 43, 43, 25, 10, 25, 25, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 43, 43, 43, 10, 25, 25, 10, 6, 1, 1, 1, 25] 43
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
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: REAL300000037932 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 1, 3, 3, 3, 1, 1, 1, 7, 11, 25, 25, 25, 1] 43
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 37, 25, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037932 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037932
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037932/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037932
Building REAL300000037933
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037933'
/scratch/stefan/7769618/working/building/REAL300000037933 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037933

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037933/0 /scratch/stefan/7769618/working/building/REAL300000037933 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1113)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1113
`/scratch/stefan/7769618/working/3D/1113' -> `0.mol2'
Preparing input files

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

`REAL300000037933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037933 none CC1=NSC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 29, 29, 29, 29, 29, 29, 29, 19, 7, 1, 1, 1, 3, 3, 3, 1] 43
rigid atoms, others: [35, 8, 10, 11, 12, 13, 14, 15, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037933 none CC1=NSC(C=NNC(=O)C2=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 29, 29, 23, 29, 29, 43, 43, 43, 29, 1, 1, 3, 3, 2, 2, 2, 6, 14, 29, 29, 23, 43, 43, 43, 29] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037933 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037933
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037933/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037933
Building REAL300000037934
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037934'
/scratch/stefan/7769618/working/building/REAL300000037934 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037934

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037934/0 /scratch/stefan/7769618/working/building/REAL300000037934 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1114)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1114
`/scratch/stefan/7769618/working/3D/1114' -> `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=CC(S(C)(=O)=O)=C1)

`REAL300000037934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037934 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 51, 51, 51, 51, 51, 51, 17, 7, 1, 1, 1, 3, 3, 3, 1] 86
rigid atoms, others: [34, 35, 36, 40, 14, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037934 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=CC(S(C)(=O)=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', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 51, 51, 37, 51, 51, 86, 86, 86, 51, 4, 4, 4, 1, 1, 1, 10, 16, 51, 51, 51, 86, 86, 86, 51] 86
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037934 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037934
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037934/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037934
Building REAL300000037935
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037935'
/scratch/stefan/7769618/working/building/REAL300000037935 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037935

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037935/0 /scratch/stefan/7769618/working/building/REAL300000037935 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1115)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1115
`/scratch/stefan/7769618/working/3D/1115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1)

`REAL300000037935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037935 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 34, 55, 55, 34, 34, 34, 34, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 12, 1, 1, 34, 55, 55, 55, 34, 34, 34, 11, 4, 12, 12, 12, 12, 1, 1, 34] 201
rigid atoms, others: [41, 42, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037935 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 201, 141, 141, 141, 141, 62, 62, 62, 28, 28, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 141, 201, 201, 201, 141, 141, 141, 62, 28, 1, 1, 1, 1, 12, 12, 141] 201
rigid atoms, others: [37, 38, 39, 40, 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, 41, 42, 43])
total number of confs: 649
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037935 none CS(=O)(=O)C1=CC=CC(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 5, 5, 5, 22, 22, 34, 34, 34, 141, 141, 141, 141, 141, 166, 166, 141, 34, 34, 1, 3, 3, 3, 1, 1, 1, 5, 22, 141, 141, 141, 141, 34, 34, 1] 201
rigid atoms, others: [32, 1, 34, 4, 5, 6, 7, 8, 9, 43, 33, 28] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 431
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037935 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037935
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037935/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037935
Building REAL300000037936
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037936'
/scratch/stefan/7769618/working/building/REAL300000037936 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037936

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037936/0 /scratch/stefan/7769618/working/building/REAL300000037936 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1116)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1116
`/scratch/stefan/7769618/working/3D/1116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1)

`REAL300000037936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037936 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 97, 149, 149, 97, 97, 97, 35, 35, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 4, 4, 1, 1, 1, 1, 98] 201
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 667
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037936 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 46, 98, 98, 47, 98, 98, 98, 98, 98, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 46, 46, 97, 98, 98, 98, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037936 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037936/1 /scratch/stefan/7769618/working/building/REAL300000037936 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1117)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1117
`/scratch/stefan/7769618/working/3D/1117' -> `1.mol2'
Preparing input files

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

`REAL300000037936.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037936/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037936 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 31, 24, 31, 31, 24, 24, 24, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 53, 53, 53, 53, 53, 53, 53, 53, 24, 24, 17, 3, 1, 1, 1, 1, 24] 53
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 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: REAL300000037936 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 20, 20, 24, 24, 20, 20, 24, 24, 24, 24, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 4, 20, 24, 24, 24, 24, 1] 53
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037936 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037936
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037936/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037936/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037936
Building REAL300000037937
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037937'
/scratch/stefan/7769618/working/building/REAL300000037937 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037937

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037937/0 /scratch/stefan/7769618/working/building/REAL300000037937 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1118)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1118
`/scratch/stefan/7769618/working/3D/1118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1)

`REAL300000037937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037937 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 45, 30, 45, 45, 30, 30, 30, 28, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 28, 28, 30, 30, 82, 82, 82, 82, 82, 82, 82, 82, 30, 30, 6, 6, 1, 1, 1, 1, 17, 17, 30] 201
rigid atoms, others: [39, 40, 41, 42, 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, 43, 44, 45])
total number of confs: 370
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037937 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 14, 30, 30, 20, 30, 30, 30, 61, 109, 115, 115, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 14, 14, 30, 30, 30, 30, 109, 109, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037937 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037937
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037937/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037937
Building REAL300000037938
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037938'
/scratch/stefan/7769618/working/building/REAL300000037938 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037938

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037938/0 /scratch/stefan/7769618/working/building/REAL300000037938 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1119)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1119
`/scratch/stefan/7769618/working/3D/1119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1)

`REAL300000037938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037938 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 38, 29, 38, 38, 29, 29, 29, 23, 23, 3, 1, 1, 1, 1, 1, 1, 6, 14, 24, 24, 1, 1, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 29, 29, 3, 3, 1, 1, 14, 14, 1, 1, 30] 201
rigid atoms, others: [39, 40, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45])
total number of confs: 311
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037938 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 13, 30, 30, 14, 29, 99, 128, 140, 140, 30, 30, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 13, 13, 29, 30, 128, 128, 30, 30, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037938 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037938/1 /scratch/stefan/7769618/working/building/REAL300000037938 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1120)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1120
`/scratch/stefan/7769618/working/3D/1120' -> `1.mol2'
Preparing input files

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

`REAL300000037938.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037938/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037938 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 61, 21, 12, 21, 21, 12, 12, 12, 8, 4, 4, 1, 1, 1, 1, 1, 1, 6, 18, 28, 28, 1, 1, 12, 12, 61, 61, 61, 61, 61, 61, 61, 56, 12, 12, 8, 4, 1, 1, 18, 18, 1, 1, 12] 201
rigid atoms, others: [39, 40, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45])
total number of confs: 304
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: REAL300000037938 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 8, 8, 12, 12, 8, 8, 36, 72, 78, 78, 12, 12, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 4, 8, 12, 12, 72, 72, 12, 12, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 297
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037938 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037938
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037938/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037938/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037938
Building REAL300000037939
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037939'
/scratch/stefan/7769618/working/building/REAL300000037939 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037939

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037939/0 /scratch/stefan/7769618/working/building/REAL300000037939 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1121)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1121
`/scratch/stefan/7769618/working/3D/1121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037939 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 35, 37, 23, 16, 23, 23, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 37, 37, 37, 37, 37, 37, 37, 35, 16, 16, 16, 10, 1, 1, 1, 1, 16] 37
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: 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: REAL300000037939 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [21, 9, 21, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 2, 4, 16, 16, 16, 16, 1] 37
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037939 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037939/1 /scratch/stefan/7769618/working/building/REAL300000037939 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1122)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1122
`/scratch/stefan/7769618/working/3D/1122' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1)

`REAL300000037939.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037939/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037939 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 77, 113, 113, 77, 77, 77, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 6, 6, 1, 1, 1, 1, 77] 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: 680
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037939 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 36, 77, 77, 77, 77, 77, 77, 85, 85, 1, 1, 16, 16, 16, 16, 16, 16, 16, 9, 1, 1, 36, 36, 77, 77, 77, 77, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037939 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037939
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037939/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037939/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037939
Building REAL300000037940
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037940'
/scratch/stefan/7769618/working/building/REAL300000037940 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037940

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037940/0 /scratch/stefan/7769618/working/building/REAL300000037940 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1123)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1123
`/scratch/stefan/7769618/working/3D/1123' -> `0.mol2'
Preparing input files

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

`REAL300000037940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037940 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 107, 142, 142, 107, 107, 107, 45, 45, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 7, 7, 7, 7, 1, 1, 1, 1, 107] 201
rigid atoms, others: [40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 613
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037940 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 16, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 39, 39, 107, 107, 39, 54, 107, 107, 107, 107, 1, 1, 16, 16, 16, 16, 16, 16, 16, 9, 1, 1, 39, 39, 39, 39, 107, 107, 107, 107, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 44, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 575
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037940 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037940/1 /scratch/stefan/7769618/working/building/REAL300000037940 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1124)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1124
`/scratch/stefan/7769618/working/3D/1124' -> `1.mol2'
Preparing input files

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

`REAL300000037940.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037940/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037940 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 35, 55, 55, 55, 55, 79, 79, 79, 109, 109, 109, 55, 55, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 35, 55, 55, 109, 109, 109, 109, 109, 109, 109, 109, 55, 1, 1, 1, 1] 109
rigid atoms, others: [1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 383
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037940 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 20, 55, 55, 40, 55, 55, 55, 55, 55, 20, 20, 20, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1, 55, 55, 55, 55] 109
rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 40, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 236
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037940 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037940
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037940/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037940/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037940
Building REAL300000037941
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037941'
/scratch/stefan/7769618/working/building/REAL300000037941 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037941

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037941/0 /scratch/stefan/7769618/working/building/REAL300000037941 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1125)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1125
`/scratch/stefan/7769618/working/3D/1125' -> `0.mol2'
Preparing input files

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

`REAL300000037941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037941 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(CC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 85, 58, 85, 85, 58, 58, 58, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 58, 58, 165, 165, 165, 165, 165, 165, 165, 165, 58, 58, 6, 6, 6, 6, 1, 1, 2, 2, 1, 1, 58] 201
rigid atoms, others: [45, 41, 42, 13, 46, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 47])
total number of confs: 571
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037941 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(CC(=O)[O-])C=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 31, 31, 58, 58, 31, 31, 89, 101, 101, 58, 58, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 31, 31, 31, 31, 58, 58, 89, 89, 58, 58, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 47, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037941 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037941/1 /scratch/stefan/7769618/working/building/REAL300000037941 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1126)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1126
`/scratch/stefan/7769618/working/3D/1126' -> `1.mol2'
Preparing input files

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

`REAL300000037941.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037941/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037941 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(CC(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 31, 61, 61, 61, 61, 89, 89, 89, 152, 156, 156, 61, 61, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 31, 61, 61, 152, 156, 156, 156, 156, 156, 156, 156, 61, 1, 1, 2, 2, 1, 1] 201
rigid atoms, others: [1, 42, 43, 46, 47, 17, 18, 19, 20, 21, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 569
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037941 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(CC(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 20, 61, 61, 20, 20, 90, 114, 114, 61, 61, 20, 20, 20, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1, 61, 61, 90, 90, 61, 61] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 15, 16, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 610
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037941 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037941
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037941/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037941/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037941
Building REAL300000037942
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037942'
/scratch/stefan/7769618/working/building/REAL300000037942 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037942

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037942/0 /scratch/stefan/7769618/working/building/REAL300000037942 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1127)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1127
`/scratch/stefan/7769618/working/3D/1127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1)

`REAL300000037942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037942 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 72, 74, 41, 36, 41, 41, 36, 36, 36, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 6, 11, 18, 18, 1, 36, 36, 74, 74, 74, 74, 74, 74, 74, 72, 36, 36, 6, 6, 1, 1, 1, 11, 11, 1, 36] 201
rigid atoms, others: [39, 40, 41, 44, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45])
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: REAL300000037942 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 13, 36, 36, 36, 36, 36, 82, 110, 123, 123, 36, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 13, 13, 36, 36, 36, 110, 110, 36, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037942 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037942/1 /scratch/stefan/7769618/working/building/REAL300000037942 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1128)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1128
`/scratch/stefan/7769618/working/3D/1128' -> `1.mol2'
Preparing input files

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

`REAL300000037942.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037942/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037942 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 51, 25, 15, 25, 25, 15, 15, 15, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 15, 22, 22, 1, 15, 15, 51, 51, 51, 51, 51, 51, 51, 49, 15, 15, 14, 6, 1, 1, 1, 15, 15, 1, 15] 201
rigid atoms, others: [39, 40, 41, 44, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45])
total number of confs: 268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037942 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(OCC(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 9, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 15, 15, 15, 15, 15, 37, 69, 71, 71, 15, 1, 1, 11, 11, 11, 11, 11, 11, 11, 9, 1, 1, 2, 6, 15, 15, 15, 69, 69, 15, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 252
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037942 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037942
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037942/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037942/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037942
Building REAL300000037943
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037943'
/scratch/stefan/7769618/working/building/REAL300000037943 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037943

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037943/0 /scratch/stefan/7769618/working/building/REAL300000037943 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1129)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1129
`/scratch/stefan/7769618/working/3D/1129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1)

`REAL300000037943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037943 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 142, 109, 142, 142, 109, 109, 109, 65, 65, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 9, 9, 1, 1, 1, 109] 201
rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 610
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037943 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 26, 109, 109, 109, 109, 109, 109, 109, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 26, 26, 109, 109, 109, 1] 201
rigid atoms, others: [32, 33, 4, 7, 8, 9, 10, 11, 22, 23, 39] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 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/7769618/working/building/REAL300000037943 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037943/1 /scratch/stefan/7769618/working/building/REAL300000037943 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1130)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1130
`/scratch/stefan/7769618/working/3D/1130' -> `1.mol2'
Preparing input files

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

`REAL300000037943.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037943/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037943 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 74, 49, 74, 74, 49, 49, 49, 30, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 105, 105, 105, 105, 105, 105, 105, 105, 49, 49, 30, 8, 1, 1, 1, 49] 105
rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 380
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037943 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 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: [17, 9, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 18, 18, 49, 49, 49, 49, 49, 49, 49, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 4, 18, 49, 49, 49, 1] 105
rigid atoms, others: [32, 33, 4, 7, 8, 9, 10, 11, 22, 23, 39] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037943 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037943
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037943/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037943/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037943
Building REAL300000037944
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037944'
/scratch/stefan/7769618/working/building/REAL300000037944 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037944

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037944/0 /scratch/stefan/7769618/working/building/REAL300000037944 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1131)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1131
`/scratch/stefan/7769618/working/3D/1131' -> `0.mol2'
Preparing input files

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

`REAL300000037944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037944 none CCC(N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 30, 74, 74, 74, 74, 110, 110, 110, 188, 201, 201, 74, 74, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11, 11, 7, 74, 74, 188, 201, 201, 201, 201, 201, 201, 201, 74, 1, 1, 1, 1] 201
rigid atoms, others: [2, 44, 45, 46, 47, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 736
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037944 none CCC(N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 1, 1, 34, 74, 74, 34, 49, 74, 74, 74, 74, 59, 59, 59, 59, 59, 34, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 1, 74, 74, 74, 74] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 43, 16, 17] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 591
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037944 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037944/1 /scratch/stefan/7769618/working/building/REAL300000037944 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1132)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1132
`/scratch/stefan/7769618/working/3D/1132' -> `1.mol2'
Preparing input files

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

`REAL300000037944.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037944/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037944 none CCC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 1, 7, 7, 40, 76, 76, 76, 76, 110, 110, 110, 164, 172, 172, 76, 76, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 40, 76, 76, 164, 172, 172, 172, 172, 172, 172, 172, 76, 1, 1, 1, 1] 201
rigid atoms, others: [2, 44, 45, 46, 47, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 669
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: REAL300000037944 none CCC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 19, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 19, 76, 76, 22, 62, 76, 76, 76, 76, 40, 40, 40, 40, 40, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 76, 76, 76, 76] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 43, 16, 17] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 522
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037944 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037944
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037944/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037944/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037944
Building REAL300000037945
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037945'
/scratch/stefan/7769618/working/building/REAL300000037945 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037945

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037945/0 /scratch/stefan/7769618/working/building/REAL300000037945 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1133)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1133
`/scratch/stefan/7769618/working/3D/1133' -> `0.mol2'
Preparing input files

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

`REAL300000037945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037945 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 23, 45, 45, 45, 45, 77, 77, 77, 133, 133, 133, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 23, 45, 45, 133, 133, 133, 133, 133, 133, 133, 133, 45, 1, 1, 1, 1] 133
rigid atoms, others: [1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 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])
total number of confs: 501
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037945 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 20, 45, 45, 45, 45, 45, 45, 50, 50, 20, 20, 20, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1, 45, 45, 45, 45] 133
rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 40, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 170
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037945 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037945/1 /scratch/stefan/7769618/working/building/REAL300000037945 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1134)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1134
`/scratch/stefan/7769618/working/3D/1134' -> `1.mol2'
Preparing input files

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

`REAL300000037945.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037945/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037945 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 137, 97, 137, 137, 97, 97, 97, 33, 33, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 5, 5, 5, 5, 1, 1, 1, 1, 97] 201
rigid atoms, others: [40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 633
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037945 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 25, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 55, 55, 97, 97, 97, 97, 97, 97, 101, 101, 1, 1, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 55, 55, 55, 55, 97, 97, 97, 97, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 44, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037945 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037945
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037945/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037945/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037945
Building REAL300000037946
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037946'
/scratch/stefan/7769618/working/building/REAL300000037946 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037946

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037946/0 /scratch/stefan/7769618/working/building/REAL300000037946 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1135)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1135
`/scratch/stefan/7769618/working/3D/1135' -> `0.mol2'
Preparing input files

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

`REAL300000037946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037946 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 49, 84, 84, 84, 84, 134, 134, 134, 201, 201, 201, 84, 84, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 49, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 84, 1, 1, 1, 2] 402
rigid atoms, others: [1, 42, 43, 44, 17, 18, 19, 20, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45])
total number of confs: 746
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: REAL300000037946 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 20, 84, 84, 84, 84, 84, 84, 84, 84, 84, 20, 20, 20, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 84, 84, 84, 168] 402
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 15, 16, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 372
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037946 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037946/1 /scratch/stefan/7769618/working/building/REAL300000037946 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1136)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1136
`/scratch/stefan/7769618/working/3D/1136' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)N=C1)

`REAL300000037946.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037946/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037946 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 137, 96, 137, 137, 96, 96, 96, 40, 40, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 8, 8, 8, 8, 1, 1, 1, 2, 96] 402
rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45])
total number of confs: 654
number of broken/clashed sets: 189
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037946 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [18, 9, 18, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 39, 39, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 18, 18, 18, 18, 18, 18, 18, 9, 1, 1, 39, 39, 39, 39, 96, 96, 96, 192, 1] 402
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 471
number of broken/clashed sets: 189
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037946 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037946
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037946/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037946/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037946
Building REAL300000037947
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037947'
/scratch/stefan/7769618/working/building/REAL300000037947 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037947

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037947/0 /scratch/stefan/7769618/working/building/REAL300000037947 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1137)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1137
`/scratch/stefan/7769618/working/3D/1137' -> `0.mol2'
Preparing input files

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

`REAL300000037947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037947 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 60, 108, 108, 108, 108, 148, 148, 148, 201, 201, 201, 108, 108, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 60, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 108, 1, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 673
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037947 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 19, 108, 108, 108, 108, 108, 108, 108, 108, 19, 19, 19, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 108, 108, 108, 108] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 40, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 230
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037947 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037947/1 /scratch/stefan/7769618/working/building/REAL300000037947 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1138)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1138
`/scratch/stefan/7769618/working/3D/1138' -> `1.mol2'
Preparing input files

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

`REAL300000037947.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037947/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037947 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 137, 103, 137, 137, 103, 103, 103, 50, 50, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 12, 12, 12, 12, 1, 1, 1, 1, 103] 201
rigid atoms, others: [40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 632
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037947 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 9, 18, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 36, 36, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 18, 18, 18, 18, 18, 18, 18, 9, 1, 1, 36, 36, 36, 36, 103, 103, 103, 103, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 44, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037947 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037947
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037947/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037947/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037947
Building REAL300000037948
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037948'
/scratch/stefan/7769618/working/building/REAL300000037948 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037948

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037948/0 /scratch/stefan/7769618/working/building/REAL300000037948 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1139)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1139
`/scratch/stefan/7769618/working/3D/1139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1)

`REAL300000037948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037948 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 147, 153, 91, 71, 91, 91, 71, 71, 71, 56, 56, 9, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 71, 71, 153, 153, 153, 153, 153, 153, 153, 147, 71, 71, 9, 9, 1, 6, 6, 71] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 513
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037948 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 9, 12, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 4, 21, 71, 71, 71, 117, 135, 135, 71, 71, 1, 1, 12, 12, 12, 12, 12, 12, 12, 9, 1, 1, 21, 21, 71, 117, 117, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 40, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 511
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037948 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037948
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037948/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037948
Building REAL300000037949
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037949'
/scratch/stefan/7769618/working/building/REAL300000037949 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037949

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037949/0 /scratch/stefan/7769618/working/building/REAL300000037949 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1140)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1140
`/scratch/stefan/7769618/working/3D/1140' -> `0.mol2'
Preparing input files

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

`REAL300000037949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037949 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 54, 75, 75, 75, 75, 121, 121, 121, 201, 201, 201, 75, 75, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 54, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201, 75, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 746
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037949 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 15, 75, 75, 75, 75, 96, 96, 75, 75, 75, 15, 15, 15, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1, 75, 75, 75] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 15, 16, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44])
total number of confs: 265
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037949 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037949/1 /scratch/stefan/7769618/working/building/REAL300000037949 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1141)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1141
`/scratch/stefan/7769618/working/3D/1141' -> `1.mol2'
Preparing input files

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

`REAL300000037949.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037949/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037949 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 134, 94, 134, 134, 94, 94, 94, 47, 47, 10, 1, 10, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 10, 10, 10, 10, 1, 1, 1, 94] 201
rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44])
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: REAL300000037949 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 27, 27, 94, 94, 94, 94, 117, 117, 94, 94, 94, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 27, 27, 27, 27, 94, 94, 94, 1] 201
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 44, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037949 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037949
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037949/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037949/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037949
Building REAL300000037950
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037950'
/scratch/stefan/7769618/working/building/REAL300000037950 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037950

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037950/0 /scratch/stefan/7769618/working/building/REAL300000037950 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1142)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1142
`/scratch/stefan/7769618/working/3D/1142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037950 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 100, 63, 100, 100, 63, 63, 63, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 140, 140, 140, 140, 140, 140, 140, 140, 63, 63, 38, 8, 1, 1, 63] 140
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])
total number of confs: 510
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037950 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 23, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 63, 63, 63, 63, 63, 63, 63, 1, 1, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 4, 22, 63, 63, 1] 140
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037950 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037950/1 /scratch/stefan/7769618/working/building/REAL300000037950 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1143)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1143
`/scratch/stefan/7769618/working/3D/1143' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037950.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037950/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037950 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 134, 98, 134, 134, 98, 98, 98, 61, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 9, 9, 1, 1, 98] 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])
total number of confs: 641
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037950 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 27, 98, 98, 98, 98, 98, 98, 98, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 27, 27, 98, 98, 1] 201
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 229
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037950 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037950
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037950/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037950/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037950
Building REAL300000037951
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037951'
/scratch/stefan/7769618/working/building/REAL300000037951 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037951

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037951/0 /scratch/stefan/7769618/working/building/REAL300000037951 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1144)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1144
`/scratch/stefan/7769618/working/3D/1144' -> `0.mol2'
Preparing input files

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

`REAL300000037951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037951 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 55, 38, 55, 55, 38, 38, 38, 28, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 38, 38, 89, 89, 89, 89, 89, 89, 89, 89, 38, 38, 28, 10, 1, 1, 1, 38] 89
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
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: REAL300000037951 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 18, 18, 38, 38, 23, 38, 38, 38, 38, 38, 38, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 4, 18, 38, 38, 38, 1] 89
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037951 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037951/1 /scratch/stefan/7769618/working/building/REAL300000037951 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1145)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1145
`/scratch/stefan/7769618/working/3D/1145' -> `1.mol2'
Preparing input files

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

`REAL300000037951.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037951/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037951 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 91, 135, 135, 91, 91, 91, 44, 43, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 6, 6, 1, 1, 1, 91] 201
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 672
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037951 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 31, 91, 91, 31, 88, 91, 91, 91, 91, 91, 1, 1, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 31, 31, 91, 91, 91, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 424
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037951 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037951
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037951/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037951/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037951
Building REAL300000037952
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037952'
/scratch/stefan/7769618/working/building/REAL300000037952 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037952

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037952/0 /scratch/stefan/7769618/working/building/REAL300000037952 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1146)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1146
`/scratch/stefan/7769618/working/3D/1146' -> `0.mol2'
Preparing input files

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

`REAL300000037952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037952 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
250  conformations in input
total number of sets (complete confs): 250
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 89, 63, 89, 89, 63, 63, 63, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 63, 125, 125, 125, 125, 125, 125, 125, 125, 63, 63, 35, 10, 1, 1, 2, 1, 63] 250
rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42])
total number of confs: 440
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037952 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
250  conformations in input
total number of sets (complete confs): 250
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 22, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 22, 22, 22, 22, 22, 22, 22, 9, 1, 1, 4, 22, 63, 63, 126, 63, 1] 250
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037952 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037952/1 /scratch/stefan/7769618/working/building/REAL300000037952 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1147)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1147
`/scratch/stefan/7769618/working/3D/1147' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1)

`REAL300000037952.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037952/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037952 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 136, 99, 136, 136, 99, 99, 99, 63, 63, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 8, 8, 1, 1, 2, 1, 99] 402
rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42])
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: REAL300000037952 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 30, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 30, 30, 99, 99, 198, 99, 1] 402
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 429
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037952 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037952
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037952/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037952/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037952
Building REAL300000037953
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037953'
/scratch/stefan/7769618/working/building/REAL300000037953 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037953

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037953/0 /scratch/stefan/7769618/working/building/REAL300000037953 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1148)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1148
`/scratch/stefan/7769618/working/3D/1148' -> `0.mol2'
Preparing input files

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

`REAL300000037953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037953 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 51, 97, 97, 97, 97, 145, 145, 145, 201, 201, 201, 97, 97, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 51, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [1, 42, 43, 44, 17, 18, 19, 20, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47])
total number of confs: 717
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037953 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 1, 1, 20, 97, 97, 97, 97, 97, 97, 97, 97, 97, 20, 20, 20, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 1, 97, 97, 97, 97, 97, 97] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 15, 16, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 196
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037953 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037953/1 /scratch/stefan/7769618/working/building/REAL300000037953 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1149)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1149
`/scratch/stefan/7769618/working/3D/1149' -> `1.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=C(S(=O)(=O)NC(C)C)C=N1)

`REAL300000037953.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037953/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037953 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 88, 42, 7, 42, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 1, 1, 88, 88, 88, 88, 88, 88, 42, 42, 42, 42, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 1] 201
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 284
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037953 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 1, 1, 1, 5, 5, 34, 34, 88, 88, 88, 88, 136, 136, 136, 201, 201, 201, 88, 88, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 88] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 8, 9, 10, 30, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 684
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037953 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037953
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037953/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037953/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037953
Building REAL300000037954
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037954'
/scratch/stefan/7769618/working/building/REAL300000037954 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037954

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037954/0 /scratch/stefan/7769618/working/building/REAL300000037954 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1150)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1150
`/scratch/stefan/7769618/working/3D/1150' -> `0.mol2'
Preparing input files

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

`REAL300000037954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037954 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 137, 118, 137, 137, 118, 118, 118, 70, 70, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 13, 13, 13, 13, 1, 1, 118] 201
rigid atoms, others: [39, 40, 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])
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: REAL300000037954 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC=C(C(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 32, 32, 118, 118, 118, 118, 118, 118, 118, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 32, 32, 32, 32, 118, 118, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037954 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037954
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037954/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037954
Building REAL300000037955
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037955'
/scratch/stefan/7769618/working/building/REAL300000037955 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037955

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037955/0 /scratch/stefan/7769618/working/building/REAL300000037955 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1151)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1151
`/scratch/stefan/7769618/working/3D/1151' -> `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=C(S(=O)(=O)NC(C)C)C=N2)N1)

`REAL300000037955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037955 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 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: [77, 77, 77, 77, 92, 92, 77, 25, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 1, 1, 77, 77, 77, 77, 77, 25, 25, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 1, 77] 201
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037955 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 53, 53, 77, 77, 77, 77, 114, 114, 114, 201, 201, 201, 77, 77, 1, 2, 2, 2, 1, 9, 9, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 77, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 702
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037955 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037955/1 /scratch/stefan/7769618/working/building/REAL300000037955 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1152)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1152
`/scratch/stefan/7769618/working/3D/1152' -> `1.mol2'
Preparing input files

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

`REAL300000037955.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037955/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037955 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 4, 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: [41, 41, 41, 41, 63, 63, 41, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 41, 41, 41, 41, 41, 22, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 41] 149
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037955 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 22, 41, 41, 41, 41, 69, 69, 69, 149, 149, 149, 41, 41, 1, 2, 2, 2, 1, 6, 22, 41, 41, 149, 149, 149, 149, 149, 149, 149, 149, 41, 1] 149
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 516
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037955 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037955
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037955/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037955/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037955
Building REAL300000037956
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037956'
/scratch/stefan/7769618/working/building/REAL300000037956 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037956

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037956/0 /scratch/stefan/7769618/working/building/REAL300000037956 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1153)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1153
`/scratch/stefan/7769618/working/3D/1153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1)

`REAL300000037956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037956 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 69, 105, 105, 69, 69, 69, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 196, 69, 69, 1, 1, 1, 1, 1, 1, 69] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38])
total number of confs: 642
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037956 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 9, 26, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 69, 69, 69, 96, 96, 69, 1, 1, 26, 26, 26, 26, 26, 26, 26, 9, 1, 1, 69, 69, 69, 69, 69, 69, 1] 201
rigid atoms, others: [4, 38, 7, 8, 9, 10, 11, 20, 21, 30, 31] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037956 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037956
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037956/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037956
Building REAL300000037957
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037957'
/scratch/stefan/7769618/working/building/REAL300000037957 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037957

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037957/0 /scratch/stefan/7769618/working/building/REAL300000037957 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1154)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1154
`/scratch/stefan/7769618/working/3D/1154' -> `0.mol2'
Preparing input files

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

`REAL300000037957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037957 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 85, 53, 85, 85, 53, 53, 53, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 123, 123, 123, 123, 123, 123, 123, 123, 53, 53, 30, 10, 1, 1, 1, 1, 53] 123
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: 460
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037957 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 23, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 4, 22, 53, 53, 53, 53, 1] 123
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037957 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037957/1 /scratch/stefan/7769618/working/building/REAL300000037957 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1155)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1155
`/scratch/stefan/7769618/working/3D/1155' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1)

`REAL300000037957.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037957/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037957 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 137, 101, 137, 137, 101, 101, 101, 62, 62, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 8, 8, 1, 1, 1, 1, 101] 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: 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: REAL300000037957 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 32, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 32, 32, 101, 101, 101, 101, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037957 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037957
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037957/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037957/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037957
Building REAL300000037958
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037958'
/scratch/stefan/7769618/working/building/REAL300000037958 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037958

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037958/0 /scratch/stefan/7769618/working/building/REAL300000037958 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1156)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1156
`/scratch/stefan/7769618/working/3D/1156' -> `0.mol2'
Preparing input files

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

`REAL300000037958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037958 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 86, 86, 86, 86, 131, 131, 131, 201, 201, 201, 86, 86, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 52, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 86, 1, 1] 201
rigid atoms, others: [1, 40, 41, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 744
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037958 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 20, 86, 86, 86, 86, 86, 86, 86, 20, 20, 20, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 86, 86] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 15, 16, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 207
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037958 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037958
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037958/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037958
Building REAL300000037959
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037959'
/scratch/stefan/7769618/working/building/REAL300000037959 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037959

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037959/0 /scratch/stefan/7769618/working/building/REAL300000037959 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1157)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1157
`/scratch/stefan/7769618/working/3D/1157' -> `0.mol2'
Preparing input files

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

`REAL300000037959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037959 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 140, 148, 80, 49, 80, 80, 49, 49, 49, 23, 23, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 49, 49, 148, 148, 148, 148, 148, 148, 148, 140, 49, 49, 4, 4, 4, 4, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2, 49] 201
rigid atoms, others: [43, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 589
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037959 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 33, 33, 49, 49, 49, 49, 49, 85, 108, 108, 49, 49, 49, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 33, 33, 33, 33, 49, 49, 85, 85, 49, 49, 49, 49, 49, 49, 1] 201
rigid atoms, others: [4, 37, 38, 7, 8, 9, 10, 11, 53, 27, 28] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037959 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037959
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037959/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037959
Building REAL300000037960
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037960'
/scratch/stefan/7769618/working/building/REAL300000037960 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037960

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037960/0 /scratch/stefan/7769618/working/building/REAL300000037960 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1158)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1158
`/scratch/stefan/7769618/working/3D/1158' -> `0.mol2'
Preparing input files

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

`REAL300000037960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037960 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)CCCCCCC(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 17, 17, 31, 37, 41, 62, 69, 108, 117, 117, 1, 1, 12, 12, 12, 12, 12, 12, 12, 8, 1, 1, 17, 17, 17, 17, 31, 31, 37, 37, 42, 42, 62, 62, 69, 69, 108, 108, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 52, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 628
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037960 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037960
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037960/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037960
Building REAL300000037961
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037961'
/scratch/stefan/7769618/working/building/REAL300000037961 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037961

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037961/0 /scratch/stefan/7769618/working/building/REAL300000037961 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1159)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1159
`/scratch/stefan/7769618/working/3D/1159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(CC(=O)[O-])C2C)N=C1)

`REAL300000037961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037961 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(CC(=O)[O-])C2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 127, 139, 59, 38, 59, 59, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 8, 13, 13, 1, 1, 38, 38, 139, 139, 139, 139, 139, 139, 139, 127, 38, 38, 1, 1, 1, 1, 1, 1, 8, 8, 1, 2, 2, 2, 38] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 43, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 44, 45, 46, 47])
total number of confs: 510
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037961 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(CC(=O)[O-])C2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 96, 116, 116, 38, 38, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 38, 38, 38, 38, 38, 38, 96, 96, 36, 38, 38, 38, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 47, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 475
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037961 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037961
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037961/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037961
Building REAL300000037962
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037962'
/scratch/stefan/7769618/working/building/REAL300000037962 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037962

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037962/0 /scratch/stefan/7769618/working/building/REAL300000037962 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1160)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1160
`/scratch/stefan/7769618/working/3D/1160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CS2)N=C1)

`REAL300000037962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037962 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 139, 109, 139, 139, 109, 109, 109, 63, 63, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 13, 13, 13, 13, 1, 1, 109] 201
rigid atoms, others: [39, 40, 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])
total number of confs: 610
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037962 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CC(C(=O)[O-])=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 28, 28, 109, 109, 109, 109, 109, 109, 109, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 28, 28, 28, 28, 109, 109, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037962 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037962/1 /scratch/stefan/7769618/working/building/REAL300000037962 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1161)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1161
`/scratch/stefan/7769618/working/3D/1161' -> `1.mol2'
Preparing input files

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

`REAL300000037962.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037962/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037962 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 58, 93, 93, 93, 93, 135, 135, 135, 201, 201, 201, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 58, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 93, 1, 1] 201
rigid atoms, others: [1, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 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])
total number of confs: 723
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037962 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 20, 93, 93, 93, 93, 93, 93, 93, 20, 20, 20, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 93, 93] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 15, 16, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 214
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037962 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037962
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037962/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037962/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037962
Building REAL300000037963
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037963'
/scratch/stefan/7769618/working/building/REAL300000037963 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037963

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037963/0 /scratch/stefan/7769618/working/building/REAL300000037963 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1162)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1162
`/scratch/stefan/7769618/working/3D/1162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)(C)C2C)N=C1)

`REAL300000037963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037963 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)(C)C2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 93, 94, 70, 50, 70, 70, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 50, 50, 94, 94, 94, 94, 94, 94, 94, 93, 50, 50, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 50] 94
rigid atoms, others: [37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 50, 51, 20, 21, 22, 23, 24, 52, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 53])
total number of confs: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037963 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)(C)C2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 9, 23, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 52, 52, 50, 50, 50, 50, 50, 1, 1, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1] 94
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 53, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037963 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037963
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037963/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037963
Building REAL300000037964
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037964'
/scratch/stefan/7769618/working/building/REAL300000037964 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037964

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037964/0 /scratch/stefan/7769618/working/building/REAL300000037964 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1163)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1163
`/scratch/stefan/7769618/working/3D/1163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])CC2C)N=C1)

`REAL300000037964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037964 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])CC2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 41, 26, 41, 41, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 26, 26, 112, 112, 112, 112, 112, 112, 112, 112, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26] 112
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47])
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: REAL300000037964 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])CC2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 40, 40, 26, 26, 26, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 112
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 47, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037964 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037964
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037964/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037964
Building REAL300000037965
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037965'
/scratch/stefan/7769618/working/building/REAL300000037965 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037965

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037965/0 /scratch/stefan/7769618/working/building/REAL300000037965 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1164)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1164
`/scratch/stefan/7769618/working/3D/1164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)C2)N=C1)

`REAL300000037965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037965 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 77, 55, 77, 77, 55, 55, 55, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 55, 55, 98, 98, 98, 98, 98, 98, 98, 98, 55, 55, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 55] 98
rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 41, 46, 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, 42, 43, 44, 47])
total number of confs: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037965 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC(C(=O)[O-])C(C)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [27, 9, 27, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 9, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 98
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 47, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037965 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037965
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037965/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037965
Building REAL300000037966
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037966'
/scratch/stefan/7769618/working/building/REAL300000037966 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037966

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037966/0 /scratch/stefan/7769618/working/building/REAL300000037966 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1165)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1165
`/scratch/stefan/7769618/working/3D/1165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1)

`REAL300000037966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037966 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 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]
0  hydrogens need rotated
201  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, 100, 141, 141, 100, 100, 100, 62, 62, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 8, 8, 1, 1, 1, 100] 201
rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 646
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037966 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 28, 100, 100, 100, 100, 101, 101, 100, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 28, 28, 100, 100, 100, 1] 201
rigid atoms, others: [32, 33, 4, 7, 8, 9, 10, 11, 22, 23, 39] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037966 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037966/1 /scratch/stefan/7769618/working/building/REAL300000037966 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1166)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1166
`/scratch/stefan/7769618/working/3D/1166' -> `1.mol2'
Preparing input files

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

`REAL300000037966.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037966/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037966 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 69, 47, 69, 69, 47, 47, 47, 26, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 103, 103, 103, 103, 103, 103, 103, 103, 47, 47, 26, 6, 1, 1, 1, 47] 103
rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 370
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037966 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CNC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 47, 47, 47, 47, 47, 47, 47, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 4, 22, 47, 47, 47, 1] 103
rigid atoms, others: [32, 33, 4, 7, 8, 9, 10, 11, 22, 23, 39] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037966 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037966
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037966/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037966/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037966
Building REAL300000037967
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037967'
/scratch/stefan/7769618/working/building/REAL300000037967 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037967

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037967/0 /scratch/stefan/7769618/working/building/REAL300000037967 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1167)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1167
`/scratch/stefan/7769618/working/3D/1167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)CC2(C(=O)[O-])CCC2)N=C1)

`REAL300000037967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037967 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)CC2(C(=O)[O-])CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 67, 47, 67, 67, 47, 47, 47, 25, 25, 6, 5, 6, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 98, 98, 98, 98, 98, 98, 98, 98, 47, 47, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 47] 98
rigid atoms, others: [41, 42, 43, 44, 45, 46, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47])
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: REAL300000037967 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)CC2(C(=O)[O-])CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 32, 32, 36, 47, 47, 47, 47, 47, 47, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 32, 32, 32, 32, 36, 36, 47, 47, 47, 47, 47, 47, 1] 98
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 47, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037967 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037967
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037967/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037967
Building REAL300000037968
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037968'
/scratch/stefan/7769618/working/building/REAL300000037968 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037968

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037968/0 /scratch/stefan/7769618/working/building/REAL300000037968 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1168)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1168
`/scratch/stefan/7769618/working/3D/1168' -> `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=C(S(=O)(=O)NC(C)C)C=N1)

`REAL300000037968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037968 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 22, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 22, 4, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 1] 190
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
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: REAL300000037968 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
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, 59, 91, 91, 91, 91, 137, 137, 137, 190, 190, 190, 91, 91, 2, 2, 2, 1, 2, 2, 2, 1, 13, 59, 91, 91, 190, 190, 190, 190, 190, 190, 190, 190, 91] 190
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 34, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 694
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037968 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037968/1 /scratch/stefan/7769618/working/building/REAL300000037968 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1169)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1169
`/scratch/stefan/7769618/working/3D/1169' -> `1.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=C(S(=O)(=O)NC(C)C)C=N1)

`REAL300000037968.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037968/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037968 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 108, 92, 39, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108, 39, 39, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 1] 201
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 330
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037968 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 48, 48, 108, 108, 108, 108, 140, 140, 140, 201, 201, 201, 108, 108, 2, 2, 2, 1, 2, 2, 2, 1, 6, 6, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 108] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 34, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 612
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037968 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037968
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037968/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037968/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037968
Building REAL300000037969
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037969'
/scratch/stefan/7769618/working/building/REAL300000037969 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037969

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037969/0 /scratch/stefan/7769618/working/building/REAL300000037969 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1170)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1170
`/scratch/stefan/7769618/working/3D/1170' -> `0.mol2'
Preparing input files

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

`REAL300000037969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037969 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [134, 130, 134, 81, 55, 81, 81, 55, 55, 55, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 55, 55, 134, 134, 134, 134, 134, 134, 134, 130, 55, 55, 34, 10, 1, 1, 1, 55] 134
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 479
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037969 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 22, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 23, 23, 55, 55, 55, 55, 55, 60, 60, 55, 55, 1, 1, 22, 22, 22, 22, 22, 22, 22, 9, 1, 1, 5, 23, 55, 55, 55, 1] 134
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037969 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037969
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037969/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037969
Building REAL300000037970
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037970'
/scratch/stefan/7769618/working/building/REAL300000037970 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037970

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037970/0 /scratch/stefan/7769618/working/building/REAL300000037970 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1171)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1171
`/scratch/stefan/7769618/working/3D/1171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=NN2C)N=C1)

`REAL300000037970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037970 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 56, 34, 56, 56, 34, 34, 34, 20, 6, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 34, 34, 86, 86, 86, 86, 86, 86, 86, 86, 34, 34, 20, 6, 1, 2, 2, 2, 34] 86
rigid atoms, others: [37, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 332
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037970 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [21, 9, 21, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 5, 19, 34, 34, 34, 34, 1] 86
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037970 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037970/1 /scratch/stefan/7769618/working/building/REAL300000037970 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1172)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1172
`/scratch/stefan/7769618/working/3D/1172' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=NN2C)N=C1)

`REAL300000037970.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037970/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037970 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 81, 124, 124, 81, 81, 81, 46, 45, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 7, 7, 1, 2, 2, 2, 81] 201
rigid atoms, others: [37, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
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: REAL300000037970 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 35, 80, 80, 90, 90, 80, 80, 80, 80, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 35, 35, 80, 81, 81, 81, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037970 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037970
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037970/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037970/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037970
Building REAL300000037971
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037971'
/scratch/stefan/7769618/working/building/REAL300000037971 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037971

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037971/0 /scratch/stefan/7769618/working/building/REAL300000037971 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1173)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1173
`/scratch/stefan/7769618/working/3D/1173' -> `0.mol2'
Preparing input files

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

`REAL300000037971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037971 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [193, 193, 193, 105, 75, 105, 105, 75, 75, 75, 45, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 75, 75, 193, 193, 193, 193, 193, 193, 193, 193, 75, 75, 45, 9, 1, 1, 1, 75] 193
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 648
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037971 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [25, 9, 25, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 75, 75, 75, 75, 101, 101, 75, 75, 75, 1, 1, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 4, 22, 75, 75, 75, 1] 193
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 302
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037971 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037971/1 /scratch/stefan/7769618/working/building/REAL300000037971 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1174)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1174
`/scratch/stefan/7769618/working/3D/1174' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1)

`REAL300000037971.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037971/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037971 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 84, 113, 113, 84, 84, 84, 50, 50, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84, 8, 8, 1, 1, 1, 84] 201
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 660
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037971 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 21, 84, 84, 84, 84, 109, 109, 84, 84, 84, 1, 1, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 21, 21, 84, 84, 84, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037971 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037971
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037971/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037971/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037971
Building REAL300000037972
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037972'
/scratch/stefan/7769618/working/building/REAL300000037972 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037972

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037972/0 /scratch/stefan/7769618/working/building/REAL300000037972 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1175)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1175
`/scratch/stefan/7769618/working/3D/1175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037972 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [187, 187, 187, 111, 77, 111, 111, 77, 77, 77, 60, 60, 9, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 1, 77, 77, 187, 187, 187, 187, 187, 187, 187, 187, 77, 77, 9, 9, 1, 1, 5, 5, 77] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42])
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: REAL300000037972 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 5, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 18, 77, 77, 77, 77, 95, 95, 101, 101, 77, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 18, 18, 77, 77, 95, 95, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037972 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037972/1 /scratch/stefan/7769618/working/building/REAL300000037972 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1176)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1176
`/scratch/stefan/7769618/working/3D/1176' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1)

`REAL300000037972.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037972/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037972 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [140, 120, 140, 56, 33, 56, 56, 33, 33, 33, 18, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 1, 33, 33, 140, 140, 140, 140, 140, 140, 140, 120, 33, 33, 18, 6, 1, 1, 12, 12, 33] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 620
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037972 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C=CC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [21, 9, 21, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 16, 16, 33, 33, 33, 33, 104, 104, 117, 117, 33, 1, 1, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 4, 16, 33, 33, 104, 104, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037972 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037972
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037972/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037972/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037972
Building REAL300000037973
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037973'
/scratch/stefan/7769618/working/building/REAL300000037973 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037973

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037973/0 /scratch/stefan/7769618/working/building/REAL300000037973 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1177)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1177
`/scratch/stefan/7769618/working/3D/1177' -> `0.mol2'
Preparing input files

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

`REAL300000037973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037973 none CC(C)NS(=O)(=O)C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 18, 33, 33, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 57, 57, 57, 57, 57, 57, 57, 57, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 18] 57
rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45])
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: REAL300000037973 none CC(C)NS(=O)(=O)C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 4, 18, 18, 18, 18, 18, 18, 18, 1] 57
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037973 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037973/1 /scratch/stefan/7769618/working/building/REAL300000037973 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1178)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1178
`/scratch/stefan/7769618/working/3D/1178' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1)

`REAL300000037973.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037973/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037973 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 18, 27, 27, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 18, 18, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 18] 45
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037973 none CC(C)NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [18, 9, 18, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 21, 21, 18, 1, 1, 18, 18, 18, 18, 18, 18, 18, 9, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 1] 45
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 45, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037973 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037973
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037973/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037973/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037973
Building REAL300000037974
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037974'
/scratch/stefan/7769618/working/building/REAL300000037974 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037974

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037974/0 /scratch/stefan/7769618/working/building/REAL300000037974 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1179)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1179
`/scratch/stefan/7769618/working/3D/1179' -> `0.mol2'
Preparing input files

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

`REAL300000037974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037974 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 97, 97, 97, 97, 135, 135, 135, 201, 201, 201, 97, 97, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 57, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 97, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 17, 18, 19, 20, 21, 22, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 698
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: REAL300000037974 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 1, 1, 20, 97, 97, 97, 97, 97, 97, 97, 97, 20, 20, 20, 4, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 1, 97, 97, 97] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 40, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43])
total number of confs: 212
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037974 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037974/1 /scratch/stefan/7769618/working/building/REAL300000037974 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1180)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1180
`/scratch/stefan/7769618/working/3D/1180' -> `1.mol2'
Preparing input files

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

`REAL300000037974.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037974/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037974 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CN=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 137, 98, 137, 137, 98, 98, 98, 51, 51, 13, 1, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 13, 13, 13, 13, 1, 1, 1, 98] 201
rigid atoms, others: [40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43])
total number of confs: 658
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037974 none CC(C)NS(=O)(=O)C1=CC=C(N=NC(C)C2=CN=CC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 33, 33, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 33, 33, 33, 33, 98, 98, 98, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 43, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037974 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037974
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037974/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037974/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037974
Building REAL300000037975
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037975'
/scratch/stefan/7769618/working/building/REAL300000037975 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037975

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037975/0 /scratch/stefan/7769618/working/building/REAL300000037975 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1181)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1181
`/scratch/stefan/7769618/working/3D/1181' -> `0.mol2'
Preparing input files

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

`REAL300000037975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037975 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 62, 47, 62, 62, 47, 47, 47, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 103, 103, 103, 103, 103, 103, 103, 103, 47, 47, 35, 7, 1, 1, 1, 47] 103
rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40])
total number of confs: 361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037975 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])N=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 4, 20, 47, 47, 47, 1] 103
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 40, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037975 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037975
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037975/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037975
Building REAL300000037976
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037976'
/scratch/stefan/7769618/working/building/REAL300000037976 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037976

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037976/0 /scratch/stefan/7769618/working/building/REAL300000037976 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1182)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1182
`/scratch/stefan/7769618/working/3D/1182' -> `0.mol2'
Preparing input files

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

`REAL300000037976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037976 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
320  conformations in input
total number of sets (complete confs): 320
using faster count positions algorithm for large data
unique positions, atoms: [160, 156, 160, 86, 65, 86, 86, 65, 65, 65, 38, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 65, 65, 160, 160, 160, 160, 160, 160, 160, 156, 65, 65, 38, 7, 1, 1, 2, 1, 65] 320
rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42])
total number of confs: 539
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037976 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
320  conformations in input
total number of sets (complete confs): 320
using faster count positions algorithm for large data
unique positions, atoms: [26, 9, 26, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 20, 20, 65, 65, 65, 65, 82, 82, 65, 65, 65, 1, 1, 26, 26, 26, 26, 26, 26, 26, 9, 1, 1, 4, 20, 65, 65, 130, 65, 1] 320
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037976 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037976/1 /scratch/stefan/7769618/working/building/REAL300000037976 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1183)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1183
`/scratch/stefan/7769618/working/3D/1183' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1)

`REAL300000037976.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037976/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037976 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 136, 94, 136, 136, 94, 94, 94, 50, 50, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 8, 8, 1, 1, 2, 1, 94] 402
rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42])
total number of confs: 670
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037976 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 28, 94, 94, 94, 94, 97, 97, 94, 94, 94, 1, 1, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 28, 28, 94, 94, 188, 94, 1] 402
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 24, 25, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 415
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037976 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037976
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037976/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037976/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037976
Building REAL300000037977
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037977'
/scratch/stefan/7769618/working/building/REAL300000037977 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037977

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037977/0 /scratch/stefan/7769618/working/building/REAL300000037977 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1184)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1184
`/scratch/stefan/7769618/working/3D/1184' -> `0.mol2'
Preparing input files

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

`REAL300000037977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037977 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 21, 21, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 59, 59, 59, 87, 87, 59, 59, 59, 59, 59, 21, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1, 59] 201
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44])
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: REAL300000037977 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 34, 59, 59, 59, 59, 95, 95, 95, 199, 201, 201, 59, 59, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 34, 59, 59, 199, 201, 201, 201, 201, 201, 201, 201, 59, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 692
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037977 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037977/1 /scratch/stefan/7769618/working/building/REAL300000037977 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1185)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1185
`/scratch/stefan/7769618/working/3D/1185' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C=C1C(=O)[O-])

`REAL300000037977.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037977/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037977 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 21, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 1, 1, 65, 65, 65, 96, 96, 66, 66, 66, 65, 65, 21, 21, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 1, 65] 201
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 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: REAL300000037977 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 51, 51, 65, 65, 65, 65, 99, 99, 99, 201, 201, 201, 65, 65, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 65, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 683
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037977 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037977
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037977/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037977/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037977
Building REAL300000037978
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037978'
/scratch/stefan/7769618/working/building/REAL300000037978 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037978

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037978/0 /scratch/stefan/7769618/working/building/REAL300000037978 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1186)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1186
`/scratch/stefan/7769618/working/3D/1186' -> `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=C(S(=O)(=O)NC(C)C)C=N1)

`REAL300000037978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037978 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 63, 65, 109, 109, 109, 109, 61, 8, 61, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 1, 1, 109, 109, 109, 109, 109, 109, 61, 61, 61, 61, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 1] 201
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 625
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037978 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 34, 34, 109, 109, 109, 109, 135, 135, 135, 201, 201, 201, 109, 109, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 576
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037978 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037978/1 /scratch/stefan/7769618/working/building/REAL300000037978 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1187)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1187
`/scratch/stefan/7769618/working/3D/1187' -> `1.mol2'
Preparing input files

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

`REAL300000037978.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037978/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037978 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 1, 9, 9, 45, 75, 75, 75, 75, 111, 111, 111, 161, 161, 161, 75, 75, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 45, 75, 75, 161, 161, 161, 161, 161, 161, 161, 161, 75, 1, 1, 1, 2, 2, 2] 161
rigid atoms, others: [1, 42, 43, 44, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47])
total number of confs: 583
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037978 none CC(=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 1, 1, 20, 75, 75, 51, 75, 75, 75, 75, 75, 75, 20, 20, 20, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 1, 75, 75, 75, 75, 75, 75] 161
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 15, 16, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 310
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037978 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037978
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037978/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037978/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037978
Building REAL300000037979
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037979'
/scratch/stefan/7769618/working/building/REAL300000037979 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037979

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037979/0 /scratch/stefan/7769618/working/building/REAL300000037979 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1188)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1188
`/scratch/stefan/7769618/working/3D/1188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1)

`REAL300000037979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037979 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 29, 31, 15, 12, 15, 15, 12, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 31, 31, 31, 31, 31, 31, 31, 29, 12, 12, 12, 8, 1, 1, 12] 31
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])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037979 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 12, 12, 12, 4, 12, 12, 12, 12, 12, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 2, 4, 12, 12, 1] 31
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 40, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037979 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037979
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037979/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037979
Building REAL300000037980
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037980'
/scratch/stefan/7769618/working/building/REAL300000037980 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037980

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037980/0 /scratch/stefan/7769618/working/building/REAL300000037980 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1189)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1189
`/scratch/stefan/7769618/working/3D/1189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=NN2C)N=C1)

`REAL300000037980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037980 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 92, 62, 92, 92, 62, 62, 62, 36, 8, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 62, 62, 131, 131, 131, 131, 131, 131, 131, 131, 62, 62, 36, 8, 1, 2, 2, 2, 62] 131
rigid atoms, others: [37, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 475
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037980 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [23, 9, 23, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 23, 23, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 5, 23, 62, 62, 62, 62, 1] 131
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037980 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037980/1 /scratch/stefan/7769618/working/building/REAL300000037980 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1190)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1190
`/scratch/stefan/7769618/working/3D/1190' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=NN2C)N=C1)

`REAL300000037980.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037980/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037980 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 144, 99, 144, 144, 99, 99, 99, 60, 60, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 8, 8, 1, 2, 2, 2, 99] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 663
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037980 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=NN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', '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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 33, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 33, 33, 99, 99, 99, 99, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037980 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037980
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037980/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037980/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037980
Building REAL300000037981
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037981'
/scratch/stefan/7769618/working/building/REAL300000037981 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037981

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037981/0 /scratch/stefan/7769618/working/building/REAL300000037981 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1191)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1191
`/scratch/stefan/7769618/working/3D/1191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CN2C)N=C1)

`REAL300000037981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037981 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 8, 5, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 139, 98, 139, 139, 98, 98, 98, 60, 60, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 8, 8, 1, 1, 2, 2, 2, 98] 201
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 659
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037981 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 8, 5, 8, 1, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 15, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 33, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1, 33, 33, 98, 98, 98, 98, 98, 1] 201
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 23, 24, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037981 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037981/1 /scratch/stefan/7769618/working/building/REAL300000037981 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1192)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1192
`/scratch/stefan/7769618/working/3D/1192' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CN2C)N=C1)

`REAL300000037981.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037981/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037981 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 145, 97, 65, 97, 97, 65, 65, 65, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 145, 145, 145, 145, 145, 145, 145, 145, 65, 65, 38, 9, 1, 1, 2, 2, 2, 65] 145
rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 526
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037981 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CN2C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [25, 9, 25, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 23, 23, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 5, 23, 65, 65, 65, 65, 65, 1] 145
rigid atoms, others: [33, 34, 4, 7, 8, 9, 10, 11, 23, 24, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037981 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037981
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037981/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037981/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037981
Building REAL300000037982
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037982'
/scratch/stefan/7769618/working/building/REAL300000037982 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037982

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037982/0 /scratch/stefan/7769618/working/building/REAL300000037982 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1193)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1193
`/scratch/stefan/7769618/working/3D/1193' -> `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=C(S(=O)(=O)NC(C)C)C=N2)O1)

`REAL300000037982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037982 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 95, 95, 67, 20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 67, 67, 67, 67, 67, 20, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1] 201
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 302
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037982 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 7, 7, 35, 67, 67, 67, 67, 108, 108, 108, 201, 201, 201, 67, 67, 1, 2, 2, 2, 1, 7, 35, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 67] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 705
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037982 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037982/1 /scratch/stefan/7769618/working/building/REAL300000037982 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1194)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1194
`/scratch/stefan/7769618/working/3D/1194' -> `1.mol2'
Preparing input files

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

`REAL300000037982.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037982/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037982 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 105, 105, 88, 21, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 1, 1, 88, 89, 89, 89, 88, 21, 21, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 1] 201
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 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: REAL300000037982 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 63, 63, 88, 88, 88, 88, 120, 120, 120, 201, 201, 201, 88, 88, 1, 2, 2, 2, 1, 8, 8, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 88] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 642
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037982 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037982
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037982/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037982/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037982
Building REAL300000037983
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037983'
/scratch/stefan/7769618/working/building/REAL300000037983 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037983

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037983/0 /scratch/stefan/7769618/working/building/REAL300000037983 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1195)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1195
`/scratch/stefan/7769618/working/3D/1195' -> `0.mol2'
Preparing input files

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

`REAL300000037983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037983 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 31, 31, 31, 31, 31, 40, 40, 12, 12, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 31, 87, 87, 87, 87, 87, 31, 12, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1] 201
rigid atoms, others: [34, 35, 44, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 419
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037983 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 31, 31, 31, 31, 55, 55, 55, 134, 176, 176, 31, 31, 1, 9, 9, 9, 9, 9, 1, 3, 15, 31, 31, 134, 176, 176, 176, 176, 176, 176, 176, 31] 201
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 25, 31] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 716
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037983 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037983
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037983/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037983
Building REAL300000037984
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037984'
/scratch/stefan/7769618/working/building/REAL300000037984 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037984

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037984/0 /scratch/stefan/7769618/working/building/REAL300000037984 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1196)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1196
`/scratch/stefan/7769618/working/3D/1196' -> `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=C(S(=O)(=O)NC(C)C)C=N1)

`REAL300000037984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037984 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 73, 73, 73, 73, 73, 73, 73, 73, 73, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 1, 1, 102, 102, 102, 73, 73, 73, 16, 4, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 1] 201
rigid atoms, others: [45, 35, 36, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037984 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 73, 73, 73, 73, 117, 117, 117, 195, 201, 201, 73, 73, 3, 3, 3, 1, 1, 1, 12, 48, 73, 73, 195, 201, 201, 201, 201, 201, 201, 201, 73] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 761
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037984 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037984/1 /scratch/stefan/7769618/working/building/REAL300000037984 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1197)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1197
`/scratch/stefan/7769618/working/3D/1197' -> `1.mol2'
Preparing input files

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

`REAL300000037984.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037984/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037984 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 75, 75, 75, 75, 75, 75, 75, 75, 75, 28, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 1, 1, 114, 114, 114, 75, 75, 75, 28, 28, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 1] 201
rigid atoms, others: [45, 35, 36, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 270
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037984 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 49, 50, 75, 75, 75, 75, 104, 104, 104, 190, 201, 201, 75, 75, 4, 4, 4, 1, 1, 1, 8, 8, 75, 75, 190, 201, 201, 201, 201, 201, 201, 201, 75] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 696
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037984 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037984
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037984/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037984/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037984
Building REAL300000037985
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037985'
/scratch/stefan/7769618/working/building/REAL300000037985 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037985

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037985/0 /scratch/stefan/7769618/working/building/REAL300000037985 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1198)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1198
`/scratch/stefan/7769618/working/3D/1198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037985 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 79, 53, 79, 79, 53, 53, 53, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 111, 111, 111, 111, 111, 111, 111, 111, 53, 53, 31, 9, 1, 1, 53] 111
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])
total number of confs: 395
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037985 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 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: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 53, 53, 53, 53, 53, 53, 53, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 4, 22, 53, 53, 1] 111
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037985 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037985/1 /scratch/stefan/7769618/working/building/REAL300000037985 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1199)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1199
`/scratch/stefan/7769618/working/3D/1199' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1)

`REAL300000037985.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037985/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037985 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 144, 106, 144, 144, 106, 106, 106, 63, 63, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 8, 8, 1, 1, 106] 201
rigid atoms, others: [36, 37, 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, 38])
total number of confs: 627
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037985 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 31, 105, 105, 105, 106, 106, 105, 105, 1, 1, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 31, 31, 106, 105, 1] 201
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037985 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037985
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037985/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037985/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037985
Building REAL300000037986
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037986'
/scratch/stefan/7769618/working/building/REAL300000037986 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037986

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037986/0 /scratch/stefan/7769618/working/building/REAL300000037986 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1200)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1200
`/scratch/stefan/7769618/working/3D/1200' -> `0.mol2'
Preparing input files

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

`REAL300000037986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037986 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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, 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: [38, 37, 38, 38, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 1, 1, 38, 38, 41, 41, 38, 38, 38, 38, 38, 38, 16, 4, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 1, 38] 86
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44])
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: REAL300000037986 none CC1=CC=C(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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, 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, 6, 6, 19, 38, 38, 38, 38, 60, 60, 60, 86, 86, 86, 38, 38, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 19, 38, 38, 86, 86, 86, 86, 86, 86, 86, 86, 38, 1] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 21, 22, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037986 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037986/1 /scratch/stefan/7769618/working/building/REAL300000037986 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1201)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1201
`/scratch/stefan/7769618/working/3D/1201' -> `1.mol2'
Preparing input files

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

`REAL300000037986.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037986/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037986 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 38, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 1, 1, 78, 78, 86, 86, 78, 78, 78, 78, 78, 78, 38, 38, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 1, 78] 201
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44])
total number of confs: 265
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037986 none CC1=CC=C(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)C(C(=O)[O-])=C1 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 6, 41, 42, 78, 78, 78, 78, 120, 120, 120, 201, 201, 201, 78, 78, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 6, 78, 78, 201, 201, 201, 201, 201, 201, 201, 201, 78, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 21, 22, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 689
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037986 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037986
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037986/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037986/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037986
Building REAL300000037987
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037987'
/scratch/stefan/7769618/working/building/REAL300000037987 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037987

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037987/0 /scratch/stefan/7769618/working/building/REAL300000037987 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1202)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1202
`/scratch/stefan/7769618/working/3D/1202' -> `0.mol2'
Preparing input files

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

`REAL300000037987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037987 none COC1=CC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 46, 46, 46, 14, 14, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 1, 1, 46, 46, 46, 46, 66, 66, 72, 72, 72, 46, 14, 4, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 1, 46, 46] 201
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037987 none COC1=CC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 31, 46, 46, 46, 46, 70, 70, 70, 152, 179, 179, 46, 46, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 31, 46, 46, 152, 179, 179, 179, 179, 179, 179, 179, 46, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 21, 22, 23, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 668
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037987 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037987/1 /scratch/stefan/7769618/working/building/REAL300000037987 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1203)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1203
`/scratch/stefan/7769618/working/3D/1203' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=CC=C1C(=O)[O-])

`REAL300000037987.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037987/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037987 none COC1=CC(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 62, 62, 62, 15, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 1, 1, 62, 62, 62, 62, 86, 86, 91, 91, 91, 62, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 1, 62, 62] 201
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 292
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037987 none COC1=CC(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 46, 46, 62, 62, 62, 62, 83, 83, 83, 141, 147, 147, 62, 62, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 6, 6, 62, 62, 141, 147, 147, 147, 147, 147, 147, 147, 62, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 21, 22, 23, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037987 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037987
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037987/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037987/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037987
Building REAL300000037988
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037988'
/scratch/stefan/7769618/working/building/REAL300000037988 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037988

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037988/0 /scratch/stefan/7769618/working/building/REAL300000037988 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1204)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1204
`/scratch/stefan/7769618/working/3D/1204' -> `0.mol2'
Preparing input files

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

`REAL300000037988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037988 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 67, 44, 67, 67, 44, 44, 44, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 44, 44, 97, 97, 97, 97, 97, 97, 97, 97, 44, 44, 28, 7, 1, 1, 44] 97
rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41])
total number of confs: 357
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037988 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 9, 21, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 18, 18, 43, 43, 43, 18, 25, 43, 43, 43, 43, 43, 1, 1, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 4, 18, 43, 43, 1] 94
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 41, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037988 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037988
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037988/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037988
Building REAL300000037989
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037989'
/scratch/stefan/7769618/working/building/REAL300000037989 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037989

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037989/0 /scratch/stefan/7769618/working/building/REAL300000037989 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1205)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1205
`/scratch/stefan/7769618/working/3D/1205' -> `0.mol2'
Preparing input files

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

`REAL300000037989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037989 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 110, 114, 114, 110, 25, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 1, 1, 110, 110, 110, 110, 110, 25, 25, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 1, 110] 201
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42])
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: REAL300000037989 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 67, 67, 110, 110, 110, 110, 138, 138, 138, 201, 201, 201, 110, 110, 1, 2, 2, 2, 1, 9, 9, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 110, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 606
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037989 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037989/1 /scratch/stefan/7769618/working/building/REAL300000037989 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1206)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1206
`/scratch/stefan/7769618/working/3D/1206' -> `1.mol2'
Preparing input files

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

`REAL300000037989.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037989/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037989 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 90, 90, 62, 21, 21, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 1, 1, 62, 62, 62, 62, 62, 21, 4, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1, 62] 199
rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037989 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 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, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 37, 62, 62, 62, 62, 104, 104, 104, 197, 199, 199, 62, 62, 1, 2, 2, 2, 1, 9, 37, 62, 62, 197, 199, 199, 199, 199, 199, 199, 199, 62, 1] 199
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 707
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037989 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037989
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037989/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037989/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037989
Building REAL300000037990
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037990'
/scratch/stefan/7769618/working/building/REAL300000037990 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037990

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037990/0 /scratch/stefan/7769618/working/building/REAL300000037990 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1207)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1207
`/scratch/stefan/7769618/working/3D/1207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1)

`REAL300000037990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037990 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
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, 23, 27, 15, 10, 15, 15, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 6, 1, 1, 10] 27
rigid atoms, others: [36, 37, 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, 38])
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: REAL300000037990 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=C(C(=O)[O-])C=CS2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [17, 5, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 2, 4, 10, 10, 1] 27
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037990 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037990
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037990/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037990
Building REAL300000037991
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037991'
/scratch/stefan/7769618/working/building/REAL300000037991 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037991

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037991/0 /scratch/stefan/7769618/working/building/REAL300000037991 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1208)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1208
`/scratch/stefan/7769618/working/3D/1208' -> `0.mol2'
Preparing input files

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

`REAL300000037991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037991 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 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]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 83, 57, 83, 83, 57, 57, 57, 34, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 57, 121, 121, 121, 121, 121, 121, 121, 121, 57, 57, 34, 6, 1, 1, 57] 121
rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 430
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037991 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 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]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [25, 9, 25, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 22, 22, 57, 57, 57, 57, 57, 57, 57, 1, 1, 25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 4, 22, 57, 57, 1] 121
rigid atoms, others: [32, 33, 4, 38, 7, 8, 9, 10, 11, 22, 23] set([0, 1, 2, 3, 5, 6, 12, 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: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037991 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037991
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037991/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037991
Building REAL300000037992
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037992'
/scratch/stefan/7769618/working/building/REAL300000037992 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037992

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037992/0 /scratch/stefan/7769618/working/building/REAL300000037992 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1209)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1209
`/scratch/stefan/7769618/working/3D/1209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037992 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 67, 52, 67, 67, 52, 52, 52, 47, 47, 8, 1, 1, 1, 1, 1, 1, 7, 9, 15, 11, 1, 52, 52, 123, 123, 123, 123, 123, 123, 123, 123, 52, 52, 8, 8, 1, 1, 7, 7, 9, 9, 52] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 448
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037992 none CC(C)NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 16, 52, 52, 52, 52, 94, 98, 107, 105, 52, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 16, 52, 52, 94, 94, 98, 98, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 44, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 410
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037992 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037992/1 /scratch/stefan/7769618/working/building/REAL300000037992 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1210)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1210
`/scratch/stefan/7769618/working/3D/1210' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1)

`REAL300000037992.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037992/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037992 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 75, 92, 39, 23, 39, 39, 23, 23, 23, 17, 5, 5, 1, 1, 1, 1, 1, 1, 8, 16, 29, 23, 1, 23, 23, 92, 92, 92, 92, 92, 92, 92, 75, 23, 23, 17, 5, 1, 1, 8, 8, 16, 16, 23] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 462
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037992 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(CCC(=O)[O-])O2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 19, 2, 1, 2, 2, 1, 1, 1, 1, 1, 4, 14, 14, 23, 23, 23, 23, 70, 90, 104, 93, 23, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 4, 14, 23, 23, 70, 70, 90, 90, 1] 201
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 44, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 478
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037992 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037992
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037992/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037992/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037992
Building REAL300000037993
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037993'
/scratch/stefan/7769618/working/building/REAL300000037993 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037993

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037993/0 /scratch/stefan/7769618/working/building/REAL300000037993 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1211)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1211
`/scratch/stefan/7769618/working/3D/1211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1)

`REAL300000037993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037993 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
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, 25, 29, 13, 10, 13, 13, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 29, 29, 29, 29, 29, 29, 29, 25, 10, 10, 10, 6, 1, 1, 1, 10] 29
rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037993 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC=CC(F)=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [17, 9, 17, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 12, 12, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 4, 10, 10, 10, 1] 29
rigid atoms, others: [34, 35, 4, 7, 8, 9, 10, 11, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037993 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037993
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037993/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037993
Building REAL300000037994
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037994'
/scratch/stefan/7769618/working/building/REAL300000037994 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037994

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037994/0 /scratch/stefan/7769618/working/building/REAL300000037994 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1212)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1212
`/scratch/stefan/7769618/working/3D/1212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C#N)=CC=C2C(=O)[O-])N=C1)

`REAL300000037994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037994 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C#N)=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 36, 21, 16, 21, 21, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 36, 36, 36, 36, 36, 36, 36, 35, 16, 16, 16, 9, 1, 1, 1, 16] 36
rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
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: REAL300000037994 none CC(C)NS(=O)(=O)C1=CC=C(NN=CC2=CC(C#N)=CC=C2C(=O)[O-])N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 2, 4, 16, 16, 16, 1] 36
rigid atoms, others: [35, 4, 7, 8, 9, 10, 11, 25, 36, 26, 42] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037994 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037994
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037994/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037994
Building REAL300000037995
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037995'
/scratch/stefan/7769618/working/building/REAL300000037995 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000037995

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037995/0 /scratch/stefan/7769618/working/building/REAL300000037995 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1213)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1213
`/scratch/stefan/7769618/working/3D/1213' -> `0.mol2'
Preparing input files

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

`REAL300000037995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037995 none CC1=NSC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 14, 14, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 1, 1, 28, 28, 41, 41, 28, 28, 28, 14, 4, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 1] 97
rigid atoms, others: [7, 8, 9, 10, 11, 12, 40, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037995 none CC1=NSC(C=NNC2=CC=C(S(=O)(=O)NC(C)C)C=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 16, 28, 28, 28, 28, 49, 49, 49, 94, 97, 97, 28, 28, 1, 1, 3, 3, 2, 2, 2, 4, 16, 28, 28, 94, 97, 97, 97, 97, 97, 97, 97, 28] 97
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 370
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037995 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037995
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037995/0.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037995
Building REAL300000037996
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037996'
/scratch/stefan/7769618/working/building/REAL300000037996 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037996

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037996/0 /scratch/stefan/7769618/working/building/REAL300000037996 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1214)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1214
`/scratch/stefan/7769618/working/3D/1214' -> `0.mol2'
Preparing input files

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

`REAL300000037996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037996 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [71, 55, 55, 55, 55, 55, 55, 55, 55, 55, 20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 1, 1, 71, 71, 71, 55, 55, 55, 20, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1] 137
rigid atoms, others: [45, 35, 36, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037996 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 55, 55, 55, 55, 83, 83, 83, 137, 137, 137, 55, 55, 3, 3, 3, 1, 1, 1, 12, 36, 55, 55, 137, 137, 137, 137, 137, 137, 137, 137, 55] 137
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 493
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037996 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037996/1 /scratch/stefan/7769618/working/building/REAL300000037996 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1215)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1215
`/scratch/stefan/7769618/working/3D/1215' -> `1.mol2'
Preparing input files

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

`REAL300000037996.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037996/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037996 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 91, 91, 91, 90, 91, 91, 91, 91, 91, 28, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 1, 1, 98, 98, 98, 91, 91, 91, 28, 28, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 1] 201
rigid atoms, others: [45, 35, 36, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037996 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(=O)(=O)NC(C)C)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 45, 46, 91, 91, 91, 91, 128, 128, 128, 201, 201, 201, 91, 91, 4, 4, 4, 1, 1, 1, 8, 8, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 91] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 670
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037996 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037996
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037996/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037996/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037996
Building REAL300000037997
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037997'
/scratch/stefan/7769618/working/building/REAL300000037997 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037997

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037997/0 /scratch/stefan/7769618/working/building/REAL300000037997 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1216)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1216
`/scratch/stefan/7769618/working/3D/1216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)C=C1)

`REAL300000037997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 97, 101, 61, 101, 101, 46, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 30, 30, 29, 1, 1, 101, 101, 101, 101, 45, 46, 1, 1, 29, 30, 30, 30, 30, 29, 30, 29, 1, 101, 101] 201
rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 453
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 198, 78, 78, 29, 29, 29, 29, 6, 1, 6, 6, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 201, 198, 198, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 29, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42])
total number of confs: 586
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 61, 62, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 117, 117, 1, 1, 1, 1, 8, 8, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037997 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037997/1 /scratch/stefan/7769618/working/building/REAL300000037997 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1217)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1217
`/scratch/stefan/7769618/working/3D/1217' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)C=C1)

`REAL300000037997.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037997/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [24, 24, 24, 16, 24, 24, 16, 16, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 23, 23, 22, 1, 1, 24, 24, 24, 24, 16, 4, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 24, 24] 54
rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 34, 22, 22, 22, 22, 6, 1, 6, 6, 1, 1, 1, 1, 1, 22, 22, 54, 54, 54, 54, 54, 34, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 22, 54, 54] 54
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42])
total number of confs: 115
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037997 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 14, 25, 25, 25, 25, 54, 54, 54, 54, 54, 54, 54, 25, 25, 1, 1, 1, 1, 4, 14, 25, 25, 54, 54, 54, 54, 54, 54, 54, 54, 25, 1, 1] 54
rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037997 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037997
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037997/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037997/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037997
Building REAL300000037998
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037998'
/scratch/stefan/7769618/working/building/REAL300000037998 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037998

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037998/0 /scratch/stefan/7769618/working/building/REAL300000037998 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1218)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1218
`/scratch/stefan/7769618/working/3D/1218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)

`REAL300000037998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 27, 1, 1, 11, 11, 11, 11, 4, 2, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 1] 43
rigid atoms, others: [32, 33, 42, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 40, 40, 27, 27, 27, 27, 27, 6, 1, 6, 6, 1, 1, 1, 1, 1, 27, 27, 43, 43, 43, 43, 40, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 27] 43
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42])
total number of confs: 74
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1C=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=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.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 5, 5, 11, 11, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 11, 11, 1, 1, 1, 1, 5, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 11] 43
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037998 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037998/1 /scratch/stefan/7769618/working/building/REAL300000037998 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1219)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1219
`/scratch/stefan/7769618/working/3D/1219' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)

`REAL300000037998.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037998/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)N2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 95, 80, 80, 80, 80, 80, 32, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 26, 26, 25, 1, 1, 80, 80, 80, 80, 32, 32, 1, 1, 25, 26, 26, 26, 26, 26, 26, 25, 1] 201
rigid atoms, others: [32, 33, 42, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)N2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 145, 58, 58, 25, 25, 25, 25, 5, 1, 5, 5, 1, 1, 1, 1, 1, 25, 25, 201, 201, 201, 201, 145, 145, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 25] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42])
total number of confs: 534
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037998 none O=C([O-])C1=CC=CC=C1CN=NC1=CC=C(S(=O)(=O)N2CCCC2)C=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', 'N.2', 'N.2', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 41, 42, 80, 80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 80, 80, 1, 1, 1, 1, 6, 6, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 80] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 664
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037998 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037998
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037998/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037998/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037998
Building REAL300000037999
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000037999'
/scratch/stefan/7769618/working/building/REAL300000037999 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000037999

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000037999/0 /scratch/stefan/7769618/working/building/REAL300000037999 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1220)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1220
`/scratch/stefan/7769618/working/3D/1220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000037999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000037999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(N=NC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [154, 74, 74, 32, 32, 32, 32, 6, 1, 6, 6, 1, 1, 1, 1, 1, 32, 32, 154, 201, 201, 183, 201, 201, 201, 201, 201, 154, 154, 154, 154, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 32, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(N=NC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 45, 45, 110, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 110, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 590
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(N=NC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 1, 1, 50, 110, 110, 68, 77, 110, 110, 110, 110, 50, 50, 50, 50, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 1, 110, 110, 110, 110] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037999 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000037999/1 /scratch/stefan/7769618/working/building/REAL300000037999 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1221)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1221
`/scratch/stefan/7769618/working/3D/1221' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000037999.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000037999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000037999/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 49, 30, 30, 30, 30, 6, 1, 6, 6, 1, 1, 1, 1, 1, 30, 30, 88, 112, 112, 112, 112, 112, 112, 112, 112, 88, 88, 88, 49, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 30, 112, 112, 112, 112] 112
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45])
total number of confs: 225
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 53, 53, 53, 53, 112, 112, 112, 112, 112, 112, 112, 53, 53, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 30, 53, 53, 112, 112, 112, 112, 112, 112, 112, 112, 53, 1, 1, 1, 1] 112
rigid atoms, others: [1, 42, 43, 44, 45, 18, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 379
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000037999 none CC(=NNC1=CC=C(S(=O)(=O)N2CCCC2)C=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 30, 1, 1, 20, 53, 53, 39, 53, 53, 53, 53, 53, 20, 20, 20, 4, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 1, 53, 53, 53, 53] 112
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 16, 17, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45])
total number of confs: 193
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000037999 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000037999
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000037999/0.*
1: /scratch/stefan/7769618/working/building/REAL300000037999/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000037999
Building REAL300000038000
mkdir: created directory `/scratch/stefan/7769618/working/building/REAL300000038000'
/scratch/stefan/7769618/working/building/REAL300000038000 /scratch/stefan/7769618/working /scratch/stefan/7769618
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000038000

mkdir: created directory `0'
/scratch/stefan/7769618/working/building/REAL300000038000/0 /scratch/stefan/7769618/working/building/REAL300000038000 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 0 (index: 1222)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1222
`/scratch/stefan/7769618/working/3D/1222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1)

`REAL300000038000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000038000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000038000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [117, 117, 117, 117, 117, 117, 26, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 30, 30, 29, 1, 1, 117, 117, 117, 26, 26, 1, 1, 29, 30, 30, 30, 30, 30, 30, 29, 1, 117] 201
rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 125, 55, 55, 29, 29, 29, 29, 6, 1, 6, 6, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 125, 125, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 29, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40])
total number of confs: 495
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(CN=NC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 69, 69, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 117, 117, 1, 1, 1, 9, 9, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 117, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000038000 /scratch/stefan/7769618/working /scratch/stefan/7769618
mkdir: created directory `1'
/scratch/stefan/7769618/working/building/REAL300000038000/1 /scratch/stefan/7769618/working/building/REAL300000038000 /scratch/stefan/7769618/working /scratch/stefan/7769618
Protomer 1 (index: 1223)
Found valid previously generated 3D confromation in /scratch/stefan/7769618/working/3D/1223
`/scratch/stefan/7769618/working/3D/1223' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1)

`REAL300000038000.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000038000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769618/working/building/REAL300000038000/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 20, 20, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 29, 29, 28, 1, 1, 48, 48, 48, 20, 4, 1, 1, 28, 28, 29, 29, 29, 28, 28, 28, 1, 48] 112
rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 112, 112, 112, 91, 91, 50, 28, 28, 28, 28, 6, 1, 6, 6, 1, 1, 1, 1, 1, 28, 28, 112, 112, 112, 91, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 28, 112] 112
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40])
total number of confs: 230
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000038000 none O=C([O-])C1=CC=C(C=NNC2=CC=C(S(=O)(=O)N3CCCC3)C=N2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 48, 48, 48, 48, 112, 112, 112, 112, 112, 112, 112, 48, 48, 1, 1, 1, 7, 29, 48, 48, 112, 112, 112, 112, 112, 112, 112, 112, 48, 1] 112
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769618/working/building/REAL300000038000 /scratch/stefan/7769618/working /scratch/stefan/7769618

Finished preparing REAL300000038000
Recording results
/scratch/stefan/7769618/working /scratch/stefan/7769618
Appending to /scratch/stefan/7769618/finished/xaaaabl.*
0: /scratch/stefan/7769618/working/building/REAL300000038000/0.*
1: /scratch/stefan/7769618/working/building/REAL300000038000/1.*
Removing working files in /scratch/stefan/7769618/working/building/REAL300000038000
/scratch/stefan/7769618
Compressing combined databse files
/scratch/stefan/7769618/finished/xaaaabl.db2.gz
/scratch/stefan/7769618/finished/xaaaabl.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7769618/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7769618/working/3D/1224'
removed directory: `/scratch/stefan/7769618/working/3D'
`/scratch/stefan/7769618/working/protonate' -> `/scratch/stefan/7769618/archive'
`/scratch/stefan/7769618/working/input-smiles.ism' -> `/scratch/stefan/7769618/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7769618/working/building'
rmdir: removing directory, `/scratch/stefan/7769618/working'
ls: No match.
ls: No match.